A method for calibrating a laser micro-machining system in three dimensions includes scanning a sample workpiece to determine the 3D surface, calculating the best fit surfaces to the scanned data in a series of steps, and storing the results so that subsequent workpieces can be calibrated to remove systematic errors introduced by variations in an associated material handling subsystem. The method optionally uses plate bending theory to model particulate contamination and splines to fit the 3D surface in a piecewise fashion to minimize the effect of local variations on the entire surface fit.