A medical robotic system having non-ideal actuator-to-joint linkage characteristics, includes a control system including a proximal control loop with actuator sensor feedback to control dynamic response of an actuator coupled to a distal joint which in turn, is coupled to an end effector to provide a degree of freedom movement of the end effector, a distal control loop with distal joint sensor feedback and feedforward to the actuator to ensure steady-state convergence of the distal joint position, and an end effector control loop with end-point sensor feedback to control the end effector position to reach a commanded end effector position.