My “Perfect” System for Storing, Organizing, Reading and Annotating PDFs

I'll be cataloging these reports tonightI have been looking for the perfect pdf reader for a long time. You may remember that earlier this year I returned the Kindle DX after it failed to live up to my requirements. Here is what I was looking for:

  • ability to highlight
  • ability to make notes
  • ability to export those notes & highlights (I like to put them in a Google docs folder so I can search them easily at any time).
  • small & portable, easy to read on a plane or carry around with me.
  • preferably e-ink, but if you can recommend a super awesome program that will work on the PC I’d consider it.

If you read the comments on the Kindle DX post you’ll see that many people recommended the iPad to me. I was hesitant to buy an iPad because no one could suggest an app that would do all the things I wanted/needed and while my technolust said that of course I needed an iPad I couldn’t really justify it given all the other devices I owned (Laptop, netbook, Kindle 3). Now remember the reason I wanted a “perfect pdf reader” was for all the reports and articles I was reading, some of which were image pdfs, I could read them on a Kindle but awkwardly and many of the pdfs that I could send to the Kindle got weirdly formatted. Fast forward a few months. I was back in school for my first semester and reading hundreds of pages of pdfs a week, many as images. Spending hours a day at the computer was killing my back, I needed a system and some tools quick! I did some reasearch and thought I’d share what I’ve found works best for me.

Over all this system was time intensive to set up, I had to learn the ins and outs of each new program and figure out how to make it do what I needed bow to my will. But in the end it was totally worth it. Here are my favorite tools and the why and how of use.


I did some research and came across PDF-XChange-Viewer for the computer. I started using the free version and loved it! With it you can:

  • add notes or comments to any pdf file
  • highlight or underline
  • export your highlights (non image pdfs) and notes – to turn on this option go to Edit -> Preferences -> Commenting and check the box next to “copy selected text to Highlight, Cross-Out….”
  • using the pencil tool you can highlight image pdfs unfortunately you can’t email or export those highlights but you can add a note retyping the text if you really want to export it later.
  • search the content of all pdfs in a folder or sub-folder.  I know Mendeley will let you search your pdfs but I use Mendeley strictly for cataloging my readings but not all my school related pdfs. For example if professors post lectures I download them as save them as pdfs for easy viewing on the iPad later.

The website has some good screenshots and videos, so I didn’t make any. It’s very robust for a free program and I’ve been very pleased with it.


Let me state for the record that I know I’m not using Mendeley to its full extent. I know it does much more I just haven’t had the time or need to figure it out. I’m using it to:

  • organize
  • catalog
  • generate citations

My massive pdf collection caused me to spend much of my holiday break renaming the files using a consistent naming system (author last name, year, then title). I then re-imported everything into to Mendeley and re-cataloged them. Yes I had to re-catalog many of them but it was important for the naming system. I can tag and assign keywords, track URLs and easily generate citations.


All of my pdfs are stored in a Dropbox folder.  This way I can access them from any of my computers and the iPad (I’ll get to it in a minute). Seriously if you are not already using Dropbox stop reading right now and go sign up, it will change your life. Dropbox allows you to save a file in a folder on your computer then access them anywhere with an internet connection including other devices. This video is a great introduction to Dropbox.

The iPad and iAnnotate

I did break down and buy an iPad mostly in an effort to alleviate my back pain from sitting at a computer reading for so long. I fretted long and hard about spending so much money for a pdf reader then paying for iAnnotate on top of it, but let me tell you once I got iAnnotate set up with Dropbox it worked so easily and beautifully that I wanted to cry (and kick my own butt for not getting it sooner!) Why I love it:

  • import and export files using Dropbox! Warns you if there is a conflict with the file in Dropbox
  • highlight, underline, etc.
  • export just your notes!
  • can “highlight” image pdfs too!
  • add text to all pdfs
iAnnotate will sync your changes to Dropbox so the next time you view the document on a computer the edits are there. [9/3/2012 edit no longer true] The one downside is that once a file is imported into iAnnotate it is no longer synced with Dropbox. This can be a problem if you important a file, make notes or highlights on the computer. For this reason I only import files I need immediately to iAnnotate, sync (or export) when done with them and delete them off the iPad. This also means I never get close to maximum space on my 16 gig iPad. iAnnotate is another robust tool I’m sure I’m not using to it’s full potential  and a quick look at the features page confirms it.
Hope this helps you find a solution to your PDF problems! Let me know if there is a tool you’re using and love that I didn’t mention.


7 thoughts on “My “Perfect” System for Storing, Organizing, Reading and Annotating PDFs

  1. I use the Notability app on the iPad for saving and annotating PDFs. Well worth the $1.99 I spent. I find it graphically cleaner, and much easier to manage for highlighting and pencil notes, than iAnnotate PDF. It also lets me rename PDFs and save them in my own categories. I don’t know how it works with Dropbox.


    1. Thanks for sharing that with the readers Lisa. I have heard of notablity but not used it. I’ve heard good things about Goodreaders as well, and hear it works with Dropbox, which was a deal breaker for me. I purchased iAnnotate almost a year ago and since it does everything I need it to and I haven’t had any problems with it, I haven’t had any incentive to spend money to try additional apps.


  2. Hi Bobbi, thanks for your sugestions . My problem is i get dry eyes if i sit infront of computer monitors and iPad for reading purpose. i use nook as it has sd card support.
    But I require 9.7-11 inch reader. Kindle DX is out of question as its discontinued, I came across M96 onyx. Have you ever got a chance to use this ?


  3. Thanks for the post!

    Regarding image PDFs, PDF-XChange Viewer can OCR them and then do pretty much everything you can do with a regular PDF.


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