It's hard to tell apart games when they're on your desktop screen, they're not just going to be named (3ds game name here) or whatnot. The only working way I know is to just copy each individual folder inside the Nintendo 3DS folder, and hope for the best. Or backup the entire mSD card, delete one folder from the mSD itself, see which game is missing, and until you get the game you're trying to backup to disappear on your 3DS, keep restoring the backup and deleting a different folder.