Why? Do we remove fingerprints from AIFIS if the accused is found "not guilty" later on? No, we do not. Nor do we expunge arrest records for criminals who are found not guilty.
Everyday in America, people are arrested because LE has found a crime scene fingerprint match to a fingerprint located in AIFIS (although it's not done nearly as quickly or efficiently as it's done on CSI:Miami). That fingerprint may have found its way into AIFIS because of a criminal arrest, a government security clearance or military enlistment package, or even because of a bond issued from a private insurance company.
Why should fingerprints, as a means of identification, be treated any differently than a fingerprint or a mugshot?
That turns out to not be true. First, if they are not guilty, they are not criminals, and second, if an arrest is made and then a person no-billed by a grand jury, the arrest record for that charge can be expunged.
I know someone that happened to. He was out more than $30K to defend himself and get his record cleaned up after a bad arrest during a nasty divorce.
/johnny