An actuator includes a motor operated by a controller through a pulse width modulation drive signal applied to a drive circuit that drives the motor. The actuator has an output shaft connected to a coupling structure for manipulating a device such as a variable geometry turbine (VGT) or an exhaust gas recirculation (EGR) valve. The device has a range of motion limited by first and second mechanical stops located at opposing low and high ends of the range. The controller learns the location of the mechanical stops during calibration. An external control unit transmits a desired position to the actuator. A protocol allows the external control unit to implicitly request a positioning mode by virtue of what value range the desired position falls into. The controller is configured to limit the drive signal to a non-harmful level when one of the positioning modes calls for pushing the device against one of the stops.