It's not incorrect to say "clean your teeth" but I've never heard this from native English speakers in normal conversation in America. At home we say "I'm going to brush my teeth." We tell our kids, "Go brush your teeth!" If they just ate chocolate we might add, "make sure you get them really clean!" However, when your dentist calls to schedule a checkup, you will hear "it's time to schedule a cleaning." It's very normal to say, "I just had my teeth cleaned at the dentist" ("dentist's office" is understood) or even "I just had my teeth cleaned" and it is understood that it was at a dentist's office.