1. Computer Skills

Beyond Highlighting: How to Get the Most From Your Annotations

Scroll to top
Read Time: 16 min

Real intellectual exchange begins when we react to what we read. The writer’s words touch our minds, sparking new ideas and questions in our minds that we'll want to come back to. But then, if you keep reading, you'll quickly forget the passage that stuck out so much the first time you read it. That's why highlights and annotations are important: they help you remember the info that stood out to you and make a trail through your book that helps you quickly rediscover the info you loved when you re-read a book or document.

In a paper book, you can underline or highlight passages, making them pop out at you the next time you read that page. Or, you can bookmark a page to easily find it again. Either way, it's rather difficult to actually get that much out of your highlights. With eBooks, though, that doesn't have to be the case at all. Your digital highlights should be far more useful than just a yellow line on your screen.

Most eBook reader apps don't make it that simple to do more with your highlights and bookmarks, so in this tutorial, I'll show you how to use the best apps for your Mac, iPad, iPhone, PC, and Android devices to get the most out of your eBook annotations.

Annotate Anywhere

Choosing a right kind of software is always a matter of your personal preference and workflow, but there's always certain specific features you need to look for when picking an app for a task. For annotation, you'll need an app that can let you:

  • View the book or document you wish to read.
  • Quickly highlight text in a color of your choice.
  • Apply labels or text to selections or highlights.
  • Add text and graphical annotations.
  • Batch search through text and annotations.
  • Export annotations.

There's a number of great apps that are designed specifically to help you get the most out of annotations, but the first point in this list is the most important: the app you use must be able to open the book you're reading. If you have a DRM free ePub or PDF eBook or document, you can make use of these better apps that we'll look at below. Otherwise, if you've purchased an eBook from the Kindle or iBooks stores, you'll need to read the books in those specific apps and use their more limited annotation tools.


Annotating eBooks on a Kindle or iPad is very easy—you'll simply tap and hold on the text you want to highlight, and select the Highlight option. What's more tricky is getting more out of your highlights. You won't find the advanced tools for annotations that you'll see in the other apps in this tutorial, but here's the options you do have for your iBooks and Kindle annotations:


iBooks lets you share individual highlights via email and social networks, but there's no built-in way to copy all of your annotations. But there's still a way to get to them if you have a Mac, using the free Digested app. Download the app, open it, and connect your iPhone or iPad via USB. You'll then see a list of all of your bookmarked and/or highlighted books. Select the books you want to copy the annotations from, then choose to save them as a PDF or export them to your Evernote library.

Copy iBooks annotationsCopy iBooks annotationsCopy iBooks annotations
Export your iBooks annotations in PDF format or send them to Evernote.

If you're using iBooks on your Mac in OS X Mavericks, you can view the iBooks annotations database on your Mac by browsing to ~/Library/Containers/ and opening the .sqlite database file—though without some serious digging, there's little you can do with that database. There's a new app, Compendiums, coming soon that will let you easily export your iBooks bookmarks from your Mac, and more, and you can signup on their site for more info if you're interested.

Or, for now, just sync your iBooks with your iOS device, and use the Digested app to copy the annotations back to your Mac. It's a roundabout way, but it does work.


If you've purchased an eBook recently, chances are you've bought it from Amazon. Their Kindle eBook library is so extensive, it even includes many standard textbooks today. And, if you're serious about annotations, you'll be glad to hear that there's a number of ways you can get your annotations out of your Kindle.

If you have an eInk Kindle (a traditional Kindle Keyboard or Kindle Paperwhite, say), the easiest way to use your annotations is to connect your Kindle to your Mac or PC with its USB cable. Browse to your Books library on the Kindle, and copy the My Clippings.txt file to your computer. You can now open your annotations in any standard text editor or word processor.

Alternately, if you use the Kindle apps on your computer, phone or tablet (or a real Kindle, of course), you can see all of your highlights online at You can see your annotations together or browse them by book, and then save the HTML page, copy the text, or use the Evernote or your other notebook tool's browser plugin to save your highlights to your notebook. Or, you can use the Bookcision tool to download your Kindle highlights in txt or PDF formats, or the Snippefy app on your iOS device to browse and export your highlights.

Kindle AnnotationsKindle AnnotationsKindle Annotations
Amazon gives you a number of ways to get your annotations off your Kindle library.


If you're reading iBooks or Kindle books, the steps above are your best option no matter what platform you're using. But if you're reading DRM-free PDF and ePub books, there's a ton of great apps to let you get the most out of your annotations.


Skim is an advanced PDF reader and annotations app for the Mac, and is my first recommendation for serious annotations. It is designed for academics, integrates with LaTeX and BibDesk for turning your annotations into a bibliography, and has great Applescript support to automate your work. Plus, it's got the great highlighting and note-taking tools you'll need to get the most from your books.

Preview of various types of annotation in Skim

You'll find the following annotation tools in Skim:

  1. Textual annotations (highlight, underline and strikethrough): helpful if you want to emphasize a particular concept or forceful statements.
  2. Vertical lines at the margin: helpful if you want to emphasize a statement already underlined or to point to a  passage too long to be underlined.
  3. Vector annotations (various shapes such as a circle, box, or freehand drawing): helpful if you want to record questions (and perhaps answers) about a passage, and to record the sequence of major points.
  4. Text notes: helpful if you want to be reminded about things that you need to do regarding the text that you read.
  5. Anchored note: helpful if you want to record longer notes, and can even include a title and icon.

When you make annotations and notes in a PDF document, they get listed in the Notes Pane. You can show/hide the pane via View → Show/Hide Notes Pane. You can filter your list of notes either by type or color of the note, or by page number. Just click the on the respective column you want to filter, and click it again to invert its order.

Preview of notes pane in Skim

Skim does not modify the original PDF file directly, but instead keeps annotations in extended attributes attached to the PDF file on disk. By default, they'll only show up on your computer; copy the original PDF to another device, and it'll have no annotations. If you'd like to sync your annotations, you can check the "Automatically save Skim note backups” option in Skim Preference. You can then view your annotations in Skim on another computer, and can even view them on your iOS device in Devonthink Pro Office since it supports Skim annotations.

Then, the most useful feature in Skim is its notes and annotations exporting tools. You can export and save your annotations separately in txt, RTF, or FDF formats, or bundle them into your PDF. The former options are a great way to review your notes on their own and use them elsewhere, and the latter is a great way to share the complete PDF document with your annotations alongside.

Various option to export notes and annotation in Skim

You can customize the way Skim exports notes in RTF or plain text formats, by adding a custom template for the export type. The template consists of a single file that should be placed in the folder ~/Library/Application Support/Skim/Templates. The name of the template files is used to describe the export type in the popup in the Export panel when you save. The file extension for the template file will also be used for the export file. You can find more info on creating custom links in the Skim wiki.

In the screenshot below, you'll see the custom templates I've added below. The first will only export the text and anchored notes from a document into rich text format, the second will export the notes along with thumbnails of each page in rich text format, and the last will export just the text and anchored notes from your PDF in rich text format. These are only a few of the ways you can customize your annotation exports in Skim.

Custom template observed in the export panel of Skim

Skim also has extensive support for scripting, using Applescript, shell scripts (sh, perl, python, ruby, and more), and Automator workflows. You can organize scripts into submenus inside Skim by adding them to subfolders in the folder ~/Library/Application Support/Skim/Scripts. Scripting Skim is beyond the scope of this tutorial, but there are already some great scripts out there to automate note processing. Check these links for pre-made scripts you can use today to get more out of your annotations:


If you've got more than just PDF books, Clearview is an easy-to-use tabbed style eBook reader that's great for annotations as well. It supports PDF, DRM-free ePub, CHM, and MOBI eBooks, so you should be able to open almost any eBook you have in Clearview. The reading view is similar to Google Chrome, and your books will open in new tabs. It doesn't have as many annotation tools as Skim, but it does do the best job of any app we've tried at rendering almost any eBook you'll come across.

Once you open a new book, you’ll be able to add bookmarks and different kinds of annotations, depending on the type of eBook you're reading:

  • PDF: Line, arrow, rectangle, ellipse, highlight, strike, underline, free text, and comments
  • ePub, MOBI, and CHM: Note/Comment, highlight, strike and underline

No matter which type of eBook you're annotating, Clearview will save the annotations in its database, and won't modify your original files. This data is saved at ~/Library/Containers/com.canoejoy.Clearview, and isn't readable by any other app. The annotations will be backed up by Time Machine on your Mac, but there's little else you can do with them. That's slightly frustrating, but at least it does include built-in export options.

Preview of various types of annotation in Clearview

Once you’ve finished annotating an eBook, click File > Export Notes... to export your highlights and more in rich text format. Clearview does not have the variety of export options as compared to Skim, but still this app does its job nicely.

Exported notes from Clearview


iBooks seems the default place to read books on the iPad, but if you're serious about annotations and are reading DRM-free eBooks, here's the best apps:


Marvin is an eBook reader for iPad and iPhone that's great for studying and annotating eBooks. It's beautiful, supports the standard eBook formats (including ePub), and can sync your books via Dropbox.

As with most apps, you can highlight text using multiple-color highlighters. You can bookmark pages, add notes (including copying and pasting text from a page), and share your annotations via email, Facebook, or Twitter. There's even two different ways to highlight passages: a simple highlight, or highlight plus which lets you change the color of highlight and add notes/comments to it.

Preview of annotation tools in Marvin

Marvin also lets you view all your bookmarks and highlights on a separate page, which makes for much easy reviewing than the preview pane that the Kindle app uses. Once you've finished annotating, you can export annotations in mrv, HTML, and CSV formats. You can also export special interchange files containing all the bookmarks, annotations, notes and vocabulary for your books. These files are useful if you want to back up annotations for a book (to import them later), share them with your friends or integrate with other reading apps that support them.

Marvin also lets you sync your annotations with Calibre, the eBook library app that's great for syncing eBooks to your devices and tweaking their metadata, using the Marvin XD plugin. It can synchronize metadata between Marvin and Calibre and let you preview and transfer highlights and annotations from Marvin to any format you want in Calibre. There's a tutorial on the Marvin blog that'll walk you through the steps you need to get the most out of your Marvin annotations in Calibre with its customizable exports.

Customization panel of MarvinXD plugin


If you're reading PDFs on your iPad, Goodreader is my app of choice. It renders PDF documents beautifully and gives you a great reading experience, and most importantly has a number of annotation tools.

The Goodreader sharing pane is in the bottom of the screen, while the Annotation tools are in right pane

To annotate a document, press and hold a finger on the text you want to select to reveal the markup options. You'll find options to add notes in the page margin with the typewriter tool, embed pop-up stickies, highlight, underline, strike out text, or call out sections with lines, arrows, shapes, or freehand drawings. It is also easy to change the color of the highlighter. There's every basic annotation tool you could want in Goodreader.

Preview of annotation tools in Goodreader app

When you begin to annotate a file, a pop-up appears prompting you to either save changes to the original file or created an annotated copy (e.g. file-annotated.pdf). Choose the latter option if you don't want to mess up the original copy. Then, once you’ve finished reading and annotating, you can either send the annotated copy to Dropbox or your other cloud storage or email it. Either way, you can send the file by itself, or with a summary of the annotations, which gives you an easy way to copy all of your highlights and notes out of the document.

Summary of notes from Goodreader. You can email this text or add it to Evernote


iAnnotate by Branchfire is another serious PDF annotations tool that runs on both iOS and Android. The annotation tools and features in this app are far beyond what most people need. Goodreader should be perfectly fine for most standard annotation needs, but if you want more or need to annotate on Android, iAnnotate is the app for you.

Preview of iAnnotate app; Settings are located in the top-right pane; Annotation tools are located in right pane

With iAnnotate, you can highlight, underline and strikethrough text, add free text with a typewriter or by hand, and add sticky notes with comments, all in lots of different colors. The app also includes tools for adding stamp markings, notes, and even photos and audio clips, useful for speaking your annotations. To add an annotation, select the text and then choose the tool you want from the context pop-up menu.

In addition to the regular mark up tools, when I edit my own work-in-progress or markup data, I often add a blank page if I want some extra space to take notes or make sketches, or to outline a new way to organize a page or a paragraph. That's a great option that you won't find in most other eBook annotation apps.

Preview of annotation tools in iAnnotate app

You can customize the toolbar to include your most-used tools, and also add additional sets of toolbars—say, for one document navigation tools, and another for document navigation tools. That's a great feature that can seriously speed up your annotations if you use some of the more hidden tools more often than the defaults.

1. Tap the (+) button  2. Select the New Custom Toolbar 3. Once you selected your preferred annotation tools tap Done.

iAnnotate also gives you a couple of great ways to review your annotations. There's another sliding panel on the left side of the app, which contains thumbnail pages of your document, as well as an outline of the document. It also includes a handy Annotations section which lists all the annotations you make in the document.

Once you’ve finished annotating a document, you can email or export the entire document with the annotations flattened and un-modifiable, or you can send the PDF un-flattened for viewing and editing in desktop PDF readers like Preview or Adobe Acrobat. And, as in Goodreader, you can send a text summary of your annotations along with the PDF to easily use your annotations elsewhere.


PDF-XChange Editor is my app of choice for reading and annotating PDFs on a Windows PC. It has an extensive suite of tools for annotating and bookmarking PDF documents. You can highlight, underline and strikethrough text, add free text with a typewriter, and add sticky notes with comments, all in lots of different colors. In addition to regular markup tools, it also includes tools for adding stamp markings and attachments.

Preview of PDF XChange Editor. The toolbar consists of various annotation tools and the left pane include Comments section.

You can customize the Comment Styles Palette via the Comments → Comment Styles Palette menu to create a collection of tools, each with the specific properties you want for quick and easy access to these variations on the default markup tools. Be sure to check the PDF-XChange tools documentation article so you can customize PDF-XChange's annotation tools to work the way you want.

PDF-XChange also includes a handy Comments section which lists all the annotations you make in the document. You can filter your list of notes/comments by the type or color of the note, or by page number. Once you’ve finished annotating a document, you can summarize comments in multiple ways, and save them to a PDF file alongside your original eBook.

Notice the number of ways this app offers to summarize comments. You can change the destination folder and file name pattern if you want

PDF-XChange doesn't include as many exporting options as Skim on the Mac, but with its customizable annotation tools, it has its own advantages for serious annotation.


There you have it: the best ways to annotate your eBooks on any platform in a way that you can export your annotations and use them elsewhere. If you're reading a PDF eBook, there's tons of great tools to get the very most out of annotations, but otherwise, even if you're using iBooks or Kindle, there's still ways to copy your annotations and use them wherever you want.

Now, when you're reading books, be sure to highlight everything that stands out to you. You're not just highlighting to be able to notice important info easily the next time you read—you're highlighting to use your highlighted info today.

Happy highlighting, and leave a comment below if you hit a snag or need help copying your annotations out of any other eBook apps!

Resources: Graphic Credit: Redaction icon designed by Dan Hetteix from the Noun Project.

Did you find this post useful?
Want a weekly email summary?
Subscribe below and we’ll send you a weekly email summary of all new Computer Skills tutorials. Never miss out on learning about the next big thing.
Looking for something to help kick start your next project?
Envato Market has a range of items for sale to help get you started.