A method is disclosed for improving the electron beam apparatus lithography process wherein the calibration procedure for the apparatus is improved by using the product pattern and stepping sequence used to make the mask on a calibration plate and/or calibration grid and to determine improved apparatus correction errors which errors are used to control the apparatus for making an improved mask. The well-known EMULATION procedure is improved by calculating additional field correction errors based on a two step registration procedure to determine X/Y apparatus stepping errors. The LEARN procedure based on a static calibration grid procedure is improved by employing the duty cycle of the product pattern to calibrate the apparatus to determine deflection beam errors.