Embodiments of the present disclosure provide a surgical robot system may include an end-effector element configured for controlled movement and positioning and tracking of surgical instruments and objects relative to an image of a patient's anatomical structure. In some embodiments the end-effector may be tracked by surgical robot system and displayed to a user. In some embodiments the end-effector element may be configured to restrict the movement of an instrument assembly in a guide tube. In some embodiments, the end-effector may contain structures to allow for magnetic coupling to a robot arm and/or wireless powering of the end-effector element. In some embodiments, tracking of a target anatomical structure and objects, both in a navigation space and an image space, may be provided by a dynamic reference base located at a position away from the target anatomical structure.