I have more than one hundred pages of handwritten notes.

I made these notes while writing different chapters of my PhD dissertation. The notes include summaries of journal articles, my thoughts, suggestions by others and anything that I thought could be potentially useful for my research.

I am wondering what is the best way to organise and store them. Converting them into pdf is one way of doing it but I want to organised them in some way e.g. by chapter, or date or key words.

Is there any program or software that can be useful in this regard?

9 Answers 9


It's not an answer, but it's too long for a comment…

I have one word for you in the future: Moleskine. Good quality notebooks, organized either thematically or chronologically, is a great way to store that sort of information. For notes, long term conservation is a big issue, and you have little guarantee that bells-and-whistles software X will still be working on your computer in 10 to 20 years. Simple solutions (both electronic and not) are the best for that purpose.

Finally, I have managed my notes electronically for some time (I tried many combinations, including iPad/Evernote/Dropbox, text files, LaTeX), but wasn't satisfied for the reasons above. I went back to dead wood storage (aka paper) with delight!

  • 4
    I love Moleskine notebooks for taking notes, and I agree, dead wood storage is great. Why not combine it with scanning and Evernote (see my reply) for easy searching! Commented Jan 16, 2013 at 21:59
  • 2
    I agree that paper storage is the ultimate future-proofed solution (especially for an individual career) but I can't imagine a near future in which a computer would't be able to read plain text. So if the OP really wants the benefits of digital (searchability, etc...) w/o any real loss of future-proofing, then simple text files is the way to go.
    – DQdlM
    Commented Jan 17, 2013 at 13:16
  • and of course, bridging the 2 most excellent worlds of Evernote and Moleskine we have this: evernote.com/moleskine
    – Shion
    Commented May 2, 2013 at 1:28
  • Good advice from F'x. I used Moleskine for years and I switched recently to (the very similar) leuchtturm notebooks (leuchtturm1917.com/en) that I discovered in a Dagsthul seminar. Pages are numbered and there is a table of contents at the beginning : it is very convenient. Commented Aug 2, 2013 at 9:02
  • One other tip would archive safe ink if you care about longer term storage of your notes. Commented Jul 17, 2017 at 16:41

I scan my notes to PDF and then use LaTeX to add a custom Table of Contents that helps with navigating the PDF.


Perhaps Qiqqa might be worth looking at.

It's a PDF / reference management system with particular emphasis (useful, novel features, not found in other such programs) on notes and links between notes on your various research papers.

...and STOP writing notes on paper! Write your notes on digital media and it'll make your life so much easier, especially WRT organization / linking / archiving / indexing...

If you're a scientist and want to keep track of notes you make, Open Notebook Science software solutions may also be worth looking at.

I wouldn't recommend EndNote. It's changed relatively little in years and years. Many of the newer PDF management systems have far better user interfaces and are in general more modern (and often free!).


I would second Evernote. They provide really great handwriting OCR, the key is to remember to scan your notes in as JPGs (or convert them to JPGs) as Evernote doesn't OCR handwriting in PDFs. With their OCR, you don't even need to organize in the app, you can just search for keywords to find what you are looking for. If you are looking for an easy way to get your notes into Evernote and you have an iPhone, I highly recommend JotNote Scanner Pro.


I use Endnote, which allows you to take pictures of the notes and put tags/dates/More Notes! on top of it.

It is very device independent, and you can do all the digitization process using an iPhone or and Android phone, of course if you have a good camera, it will be better for the resolution issues.

There is a company that does OCR for Endnote compatibility, but you have to buy their special paper, which is a bit pricey.

  • I want to make sure OCR stands for Optical Character Recognition? If yes, does that company's paper work for Chinese/Japanses?
    – Nobody
    Commented Jan 16, 2013 at 7:49
  • I do not know if it works, but you can use Acrobate Professional after taking the picture/scanning and use Adobe's OCR, I've used it before with good results for Japanese Kanji Commented Jan 16, 2013 at 7:55
  • 3
    Are you sure you mean Endnote, and not Evernote?
    – Eekhoorn
    Commented Jan 16, 2013 at 9:17
  • Surely "Evernote"?? "Endnote" is not good.
    – Peter K.
    Commented Jan 16, 2013 at 15:30
  • A lot of OCR doesn't work well with handwriting...Evernote OCR on the other hand does! Commented Jan 16, 2013 at 22:00

You could also have a look at Evernote, this does a nice job of organizing notes. I think it even supports making pictures with the Evernote app (android or iphone), and upload it (e.g. for a poster on a conference). I use to store computer typed notes, but you could also upload and store scanned handwritten notes. Evernote has a free account with limited bandwith, so depending on what you want this might or might not be enough.


Since you already have the notes written, it seems that mainly what you are looking for is a digital reference management system - akin to the digital card catalogs of the library.

This would allow you to search your notes for a key word or subject and then know that it is in notebook A on page 20. There would be lots of ways to do this but zotero is very flexible and should be able to accommodate your needs.


Even though this thread is old, this may be helpful info. You can use the Onenote program incuded in MS Office. It tries to do OCR on any document you either scan and drop into a Onenote page or "print" from pdf into a Onenote page. For notes that it cannot OCR, you can add annotations with searchable keywords. To separate pages of a large pdf document you can use a program like PDFill Free. Not a perfect solution, but can still be a big help in making handwritten notes into electronically searchable documents.


I would scan them and save them to evernote. An alternative is that you find a freelancer (for example on odesk) that types your notes (software is not very good at recognizing handwriting).

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