Various methods for performing various surgical procedures using a robotic instrument system are disclosed. In one embodiment, the method comprises advancing a guide instrument into a patients body and to the vicinity of a treatment area. The guide instrument may be a robotically controlled catheter which is controlled by a robotic catheter system. The guide instrument comprises an elongate flexible body having a proximal end and a distal end, and an end effector coupled to the distal end. The end effector may comprise various devices for assisting and performing the surgical procedure. For example, the end effector may be a clip applier, a laser fiber, a cryo fiber, or a needle and grasper. An image capture device may also be coupled to the distal end to assist in positioning and operating the guide instrument.
