Methods and systems for verification of a mark written on a target surface during a multiple beam lithography process, and for verifying beam position of individual beams on the target surface based on mark verification are disclosed. A mark can be verified by scanning an optical beam over the mark and measuring the reflected optical beam and the position of the target with respect to the optical beam. By comparing the intensity of the reflected light as a function of distance over the mark with reference mark data representing an intended definition of the mark, and any deviation between the measured representation and the reference mark data are determined. If any deviation deviate more than the predetermined limit, incorrectly positioned beams can be verified from the data.