This feature has been fixed in PaperScan 1.4.
You can define a region of scan using the WIA protocol: In the scanning wizard, just click the button "..." near the page size. See attached screenshot.
@sebthemonster, If the "adavanced options" button is unactivated it is because your TWAIN driver doesn't provide GUI to control device parameters. Into a future release we will try to implement the Image layout configuration for TWAIN drivers.
@tasgolf72, I answered to your ticket on the helpdesk. Please try to don't duplicate the same support request on forum & helpdesk.
PS 1.4.4 has been released with the desired improvements.
See change log: http://www.orpalis.com/products/paperscan/history/
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