A method of calibrating a laser marking system includes calibrating a laser marking system in three dimensions. The step of calibrating includes storing data corresponding to a plurality of heights. A position measurement of a workpiece is obtained to be marked. Stored calibration data is associated with the position measurement. A method and system for calibrating a laser processing or marking system is provided. The method includes: calibrating a laser marker over a marking field; obtaining a position measurement of a workpiece to be marked; associating stored calibration data with the position measurement; relatively positioning a marking beam and the workpiece based on at least the associated calibration data; and calibrating a laser marking system in at least three degrees of freedom. The step of calibrating includes storing data corresponding to a plurality of positions and controllably and relatively positioning a marking beam based on the stored data corresponding to the plurality of positions.