A medical navigation system is provided having a positioning device having a positioning arm with a flange at the end of the positioning arm, a controller at least electrically coupled to the positioning device, and an end effector joystick controller for connecting to the flange of the positioning arm. The controller has a processor coupled to a memory and a display. The end effector joystick controller includes a mating component for connecting to the flange of the positioning arm, and a joystick portion extending from the mating component.