A method of generating control commands to be executed by a motion control system under control of a plurality of system users to move an object in a desired manner. At least one restricted program element associated with the motion control system is identified. An application program used by the system users when controlling the motion control system is provided. The application program employs the at least one restricted program element. A plurality of access levels are determined. Each restricted program element is associated with one of the access levels. Each of the plurality of system users is associated with one of the access levels. Motion control commands are generated based on the application program, the access level of each system user, and the access level of each restricted program element.