Described herein are multi-part instrument systems and methods of use. The instrument can include an inner and outer body member where the inner body member is adapted to dock with the outer body member. When docked, driving the outer body member via a manipulation section can control the inner body. In use, an inner body member can be removed and replaced by a different inner body member to change the tool end effector. Alternatively, driving a manipulation section of the inner body member can control the outer body member. The outer body member can be disposable while the inner body member is reusable.