A search for 'Barcode' on CPAN reveals plenty of modules for *creating* barcodes, but virtually nothing for reading them in again...it presumably is possible, but a lot would depend upon how your scanner creates them - either as a series of vectors or as a bitmap, I would presume. If the latter, you might be able to read in the image with GD and do some pixel-munching, but it sounds like a task-and-a-half.
in reply to Digital Document Capture
I don't know anything about your ScanToEmail machine, but would there be any way of spitting out the actual barcode number as part of the scanning process? Say, put the number into the Subject header or something?