A robotic catheter system includes a controller with a master input device. An instrument driver is in communication with the controller and has a elongate instrument interface including a plurality of instrument drive elements responsive to control signals generated, at least in part, by the master input device. An elongate instrument has a base, distal end, and a working lumen, wherein the guide instrument base is operatively coupled to the guide instrument interface. The elongate instrument preferably comprises and/or defines other lumens to accommodate instruments such as an optics bundle, a light bundle, a laser fiber, and flush irrigation. The working lumen preferably is configured to accommodate a grasping or capturing tool, such as a collapsible basket or grasper, for use in procedures such as kidney stone interventions. The elongate instrument includes a plurality of instrument control elements operatively coupled to respective drive elements and secured to the distal end of the instrument. The instrument control elements are axially moveable relative to the guide instrument such that movement of the guide instrument distal end may be controlled by the master input device.