The present invention provides an apparatus and improved method of friction stir spot welding that assures a predetermined bottom thickness and a reduction in variation in a series of resultant spot welds. The advantage of the present invention lies in that the plunge distance is controlled from the top plane of the anvil against which the bottom thickness is specified, and systematically adjusted to account for changing system parameters, such as, but not limited to, deflection and thermal expansion of the weld gun. The present invention also provides for improved and controlled weld quality through implementation of a dwell operation or dwell operations, whereby weld heat input is manipulated by causing the weld tool to dwell in a dwell region or at a desired depth or depths within the workpiece(s) for a predetermined time interval to achieve desired mechanical properties of the resultant weld joint.