I am pretty sure that ours go to the state level, where they are kept on file forever.
The dozens of fingerprint cards I did from the military went to federal level files for military rcords or security clearances, and are cross-linked with the FBI's database. The state level cards I did for my Peace Officer license and commissioning as a Peace Officer also go to the state level and are on file and are cross-linked witht he same databases as the criminal ones.
Anyone being jailed for an offense with a possible punishment of jail time (and not just fine-only offense like Public Intoxication) is supposed to have a print card taken and the card is maintained at the state level and linked with criminal history records. Crimanl History records usually contain a Fingerprint Classification, a series of codes that tell a latent examiner what the characteristics of a fingerprint are without actually having a comparison print.