IIRC for some reason I had to go twice downtown. First you have to file your paperwork, and pay the fee ($10?) Thenyou wait a couple days while theyrun the background check and they 'schedule' your fingerprinting on a later date.
It's wasall done at the courthouse downtown though, at least it was three years ago. They've now moved some services to city center at oyster point.
bottom line, I'd call ahead.