A methods using a robotic catheter system to perform a procedure on a patient includes generating a control signal corresponding to movement of a master input device, and moving a plurality of drive elements of an instrument driver in response to the control signal, the drive elements operatively coupled to a corresponding plurality of control elements of an elongate guide instrument, the control elements secured to a distal end of the guide instrument and moveable axially relative to the guide instrument such that movement of the drive elements causes a corresponding movement of the guide instrument distal end.