A document scanner (10) includes an input tray (30) for holding documents (20) and an input image capture device (40) for capturing images of the documents (20)in the input tray (30) prior to transporting the document for imaging; an output tray (150) for holding documents (20) after the documents (20) exit the scanner; an output image capture device (140) for capturing images of the output tray; an image processor for determining characteristics of the output tray or characteristic of the documents (20) before imaging and after the documents (20) exit the scanner; and scanner functions are modified based on the output tray characteristics or the document characteristics.