Managing & Annotating PDFs in Evernote

An Updated System

Anthony Draper
4 min readOct 4, 2018


Several months ago, I wrote an article about how I scan, annotate, and store my PDFs using Noteshelf 2 and Evernote.

“flat lay photography of blue backpack beside book and silver MacBook” by Matt Ragland on Unsplash

Since then, I’ve graduated from undergrad and started law school. Consequently, my PDF usage and needs has gone way up, and the old system simply wasn’t cutting it. If you didn’t catch the old article, here’s a basic rundown.

  • Scan the document or access it online
  • Open it in Noteshelf 2
  • Annotate it as needed
  • Sync the notebook to Evernote

This worked fairly well, but as some of you pointed out, the handwriting wasn’t OCRd in Evernote like the rest of my Evernote notes, and this made it significantly less useful long-term.

Noteshelf is also primarily not a PDF annotation app, it’s a note taking app. So it worked great to markup a document, but doing anything with those markups wasn’t possible. In this way, there was no difference between marking it up on paper and scanning it and scanning it then marking it up — the end result was the same. While I note some specific benefits of using Noteshelf that don’t transfer to this new method, such as the annotation summary, I think that there are different features below that make those ones redundant, even if it might not be immediately obvious.

These days, I need to read and brief three or four cases each day. Ideally, I need that information to be searchable, clear, and organized. I also needed to link it to my other notes on legal concepts, other cases, and lectures so I know what connects with what. Noteshelf simply wasn’t cutting it.

I briefly tried Microsoft OneNote, but I just couldn’t stick with it. It may have been aesthetic reasons, it may have been that that app’s method of organization just didn’t work with my brain, but I couldn’t keep it up.

I desperately wanted to use Evernote. So I went hunting, and I found the perfect app for my PDF/Evernote needs.

MarginNote has been around for a while, but in the last few months, the developer has released a complete overhaul, MarginNote 3. Available for MacOS and iOS, this app will answer your PDF prayers if you’ve been frustrated with Evernote-PDF integrations for the last ten years.

Like a fair few other PDF apps, the app allows you to highlight text, either selecting actual text or drawing over it. You can add comments, write in the margins, and do all the ordinary PDF annotation things you’d expect. But the app has a couple magnificent features.

  1. If you’re working with a scanned PDF that hasn’t been OCRd, this app will OCR any highlights you make and grab the text for you.
  2. You can “merge” highlights, so if you have a continuous highlight across multiple pages, you can simply highlight the text on the first page, then the text on the second, and select “merge.” The text then shows up in the “notes” window as one highlight. (Why don’t more apps do this?)
  3. Not only can you write/highlight directly on the document with Apple Pencil (or your finger,) but you can handwrite in the comments boxes that you make. This one really blew me away. But it gets better.
Highlights and handwritten comments in MarginNote

4. Once you’ve made all your highlights, annotations, and comments, you. simply select “Export to Evernote” and it sends the document as a PDF to Evernote in a new note in whichever notebook you desire. It then inserts, chronologically, all of your highlights and notes, even the handwritten ones! And of course, this is all searchable. So in one note, you have the marked-up PDF and all of your highlights and comments listed as text.

Excerpts and comments exported into Evernote.

These features are the ones that really sold me on the app. However, there are a host of other features that users may enjoy, such as the ability to create extensive mind maps from highlights and notes, including the ability to put annotations from multiple documents in one mind map.

What are your experiences with Evernote and PDFS?




Anthony Draper

Graphomaniac interested in culture, philosophy, and theology. Support my efforts: