A medical instrument with an elongated outer housing and inner drive shaft and including an instrument flushing system that enables the medical instrument to be effectively cleaned after use is disclosed. The medical instrument may be configured such that the instrument flushing system receives a flushing fluid through a port at a proximal end of the instrument and directs the flushing fluid through a flushing fluid plenum created between an inner surface of the elongated outer housing and an outer surface of the inner drive shaft. The flushing fluid plenum may be maintained by a standoff formed from a collar with one or more axially extending grooves. The instrument flushing system may include a seal to seal portions of a drive system in communication with the inner drive shaft and extending radially outward from a main body of the medical instrument.
