The scanning apparatus linearization and calibration system includes an electromechanical scanner having a sample stage portion, and a deflecting member, mounted between the scanning means and a fixed mounting member, that undergoes deflection in response to displacement of the scanner sample stage portion in at least one dimension of displacement. Strain gauges are mounted to the deflecting member for measuring the deflection of the deflecting member and for generating a deflection output signal indicative of an amount of deflection of the deflecting member, to provide a highly sensitive indication of actual displacement of the sample stage of the scanning apparatus. Control circuitry also provides for open loop displacement correction and for closed loop feedback correction of the position of the scanner sample stage.