As one who just went through this whole shebang...basic 135 pax charter no...if you are flying as a feeder/contract for UPS/FedEx/DHL/etc, then yes. Not only prints but a CHRC...Criminal History Records Check.  If your company is a NATA member you can get a break on the CHRC.  Fingerprinting is easiest down with your local PD (Unless you're in big town/city ala LA, SFO, SAC, etc.)
UPS initiated this for their small feeder contract companies due to, what the TSA called a "security gap" when the packages left the "safety" of the brown trucks into and unknown (read unsafe/non-terrorist-proof) small feeder aircraft.  (Who knows what devious plans those fr8dawgs have in mind!)  TSA said "Fix it" so UPS proposed the CHRC/Fingerprinting deal.  TSA said, "Thanks for making policy for a federal agency".  Small feeders for UPS had to complete all of the process by the end of March.
Eric