An electronic device manufacturing system includes a motion control system for calibrating a gap between surfaces of process chamber or loadlock components by moving those component surfaces into direct contact with each other. The component surfaces may include a surface of a substrate and/or a substrate support and a surface of process delivery apparatus, which may be, e.g., a pattern mask and/or a plasma or gas distribution assembly. The motion control system may include a motion controller, a software program executable by the motion controller, a network, one or more actuator drivers, a software program executable by the one or more actuator drivers, one or more actuators, and one or more feedback devices. Methods of calibrating a gap via direct contact of process chamber or loadlock component surfaces are also provided, as are other aspects.