[Jobu]

I wait until I have multiple items to scan and then put them all on the scanner at once, flip them and do the backs. I then use the free Photoshop-like software Paint.net to open them and cut and paste the individual front-backs into new files that I then save with the card's set, name, and another detail or two if I might have files with the same name.

Also - scanners will make images that are way higher resolution than you need to have a nice scan. I try to have the final individual card files end up at about 1 MB - they look great and are the right size to be posted here without needing to create a smaller file.