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You might look into Optical Mark Recognition (OMR) for your scanner.
Some scanners even come with it.
You don't really say how these forms are marked but the current software is pretty advanced.
Just do a search using FileMaker OMR ....
Any chance that you could put the questionnaires online as a form on a website and have the form data emailed to you?
For example, I use a program called Forms to Go which creates a PHP script to forward the html webpage form data to me by email.
We've tried using an online questionnaire. The completion rate for students filling in the questionnaire is low when they are given a weblink. During class time it is difficult to administer as trainers need to provide students access to a computer terminal. A good idea in principal, but won't work for our situation.
Thank you for your suggestion.