This is the way our Masterwood works. The barcode is the name of the file (barcode is just a font) with an * before and after the filename, presumably to aid in finding the start and end of the filename?? So you'd need Mach3 to read the input from the scanner, and pass that filename to the plugin or script that is waiting to open the file. Our machine will run the program, then remove it and wait for the next scan. It has to be put into barcode mode before it works. Not sure if this helps or not.
How do you plan on creating the bar codes? We use CadCODE, which converts .dxf's to machine code, and adds the barcode info into an optimized cutlist for a CNC saw, which prints barcoded labels for the parts while they are being cut.