A method of operating a manipulator arm comprising a manipulator interface configured to removably couple with and transmit actuation force to a medical instrument includes mounting a cannula to a cannula mount coupled to the manipulator arm; mounting a medical instrument to the manipulator interface; inserting a shaft of the medical instrument through an entry guide mounted to the cannula; rotating the manipulator interface and the medical instrument relative to the cannula mount; and rotating the entry guide relative to the cannula mount about a longitudinal axis of the cannula.