Acrobat ClearScan + Preview.app

Hi Akira,

I do have the same problem and did some research through various message boards. Apparently Apple's Preview viewer deletes the non-system font information that is put in the PDF file by Acrobat while doing a 'Clearscan'. So as soon as you save the file using Preview, you unknowingly delete all the information on the text 'behind' the visible characters. This is a huge issue for me as I highlight through a lot of PDF documents which I receive from various sources and many of the older documents are scanned using Acrobat's Clearscan feature to restore smooth fonts and drastically reduce the size of the documents.

One solution is to stop using Apple's Preview tool and use another tool. Some have mentioned that Skim provides annotations in a different file without affecting the source PDF. Another solution if you have access to Acrobat (for which there is a 30 day trial option) is to save the document to a TIFF image file and then re-OCR the file using the 'retain image' option. The disadvantage is that this file will be much bigger and slower to scroll if you want reasonably smooth text. If you do this, you should set the properties for output to TIFF and convert to PDF options to use 600dpi (or at least 300dpi) and use lossless compression on images so that your text stays nice looking. If you ensure that your TIFF output is in black-and-white the file shouldn't be ridiculously large.

Hopefully they will fix that problem with Preview soon. The improvements made to the highlighting feature of Preview made an essential tool for my daily work and that of many other academics.