Directed energy beam deflections are compensated by mapping pixel coordinates of an image of a patterning field to patterning field spatial coordinates. For example, electron beam scanning is compensated by imaging calibration features defined on a reticle to produce a mapping between pixel and physical coordinates. An electron beam is scanned to produce cathodoluminescence at a plurality of scan locations in a patterning field. With the pixel coordinate mapping, an image of the cathodoluminescence is used to determine compensated scan drive values. Other directed energy beam deflections can be similarly compensated.