You need Adobe Acrobat not Adobe reader. Other PDF tools do not have such feature.
This is a bit tricky but so simple:

1-The basic requirement
What Acrobat Pro can do is not to directly extract the highlighted text, but the text that is inside a comment box (i.e. annotations). Therefore, the first thing you have to do is to change one of the preferences of Acrobat Pro to copy the text that you highlight into a comment box or pop-up. To activate this feature:

1. Open Acrobat Pro and go to Edit and then Preferences (or press CTRL + K).
2. Choose the Commenting category.
3. Activate the option “Copy selected text into Highlight, Cross-Out, and Underline comment pop-ups”.
4. Click OK.

From now on, every time you highlight text in Acrobat Pro, a comment pop-up will be created. The highlighted text will be pasted on that pop-up without any additional action.

2-Export your comments as "*.fdf" file then use below tool. Just simply drag fdf file to the "FDF Text Extractor.exe". A text file containing your highlights will be created.
http://www.desiquintans.com/fdfextract

It works for me.

 

Last edited by a moderator: Feb 25, 2016