Don'tcha watch NCIS? The Feds got something called IAFIS, Integrated Automated Fingerprint Identification System. They scan the prints into the system and the computer compares yours to every one in the database. If you are already on file it verifies you are who you say you are, it also checks against all the "unknowns" recovered from crime scenes to possibly link you to an unsolved crime. If you weren't in the database before, you will be after they "run your prints". They even have mobile scanners now so agents can run your prints in the field in reatime.
FBI — IAFIS