A method of calibrating the beam position in a charged-particle beam system starts with finding a focus deviation on the material surface for each point within a deflection field. A focus correction voltage VF necessary to cancel out the focus deviation is determined. A beam position deviation fi per unit focus correction voltage is found. The deflection voltage is corrected so as to cancel out the product fi·VF. The deflection voltage is corrected so as to cancel out the sum of the product fi·VF and the measured deflection field distortion while correcting the focus based on the voltage VF.