A system includes a manipulator arm configured to support an instrument having an end effector, the manipulator arm including a distal portion, a proximal portion coupled to a base, and a multitude of joints between the distal portion and the base, the multitude of joints providing sufficient degrees of freedom to allow a range of differing joint states of the multitude of joints for a state of the distal portion. The system also includes a processor coupled to the manipulator arm. The processor is configured with a manipulation mode and a clutch mode, the clutch mode selected from the group consisting of: an arm-null-perpendicular-clutch mode, a port-null-perpendicular-clutch mode, and an arm-port-null-perpendicular-clutch mode. The processor is configured to operate the multitude of joints in accordance with at least one of the manipulation mode and the various clutch modes.