A robotic medical instrument system for driving a segment of a catheter or other instrument. A segment, such as the distal end, of a catheter may be axially and/or rotatably driven. Drive elements include an internal and retractable catheter drive shaft, an actuation element coupled to an internal portion of the catheter body and including an internal guide in which a pin can move to drive a gear and rotate the catheter, a harmonic drive element, a wobble plate drive element, and a planetary gear drive element.