Once upon a time there were different types of notes issued. Each had a different color of ink. There were gold certificates, silver certificates, US notes, federal reserve notes, and maybe one or two others. The different color ink designates what it is without actually having to read it, although that information will be printed on it somewhere. Current bills are federal reserve notes.
Do you mean like a red mark at the top of the bill?? If so banks often use this method to keep track of money as it is in their teller drawers. Ity can be used as bait...although most banks usually use 20s as bait.....