A robotic instrument system having a controller including a master input device (12), and an instrument driver (16) in communication with the controller. The instrument driver includes a guide instrument interface including two or more guide instrument drive elements responsive to control signals generated, at least in part, by the master input device for manipulating a guide instrument operatively coupled to the instrument interface, and a sheath instrument interface including two or more sheath instrument drive elements responsive to control signals generated, at least in part, by the master input device for manipulating a sheath instrument operatively coupled to the instrument interface, wherein the sheath instrument drive elements are control independently of the guide instrument control elements.
