In a particle projection lithography system, an alignment system is used to determine alignment parameters to measure the position and shape of an optical image of a pattern of structures formed in a mask and imaged onto a target by means of a broad particle beam, by means of an apparatus with a plurality of alignment marks adapted to produce secondary radiation upon irradiation with radiation of said particle beam. In order to allow for a variation of the alignment parameters along the optical axis, the alignment marks are positioned outside the aperture of the alignment system for the part of the beam that generates said optical image, arranged at positions to coincide with particle reference beams projected through reference beam forming structures provided on the mask while said optical image is projected onto the target, and situated on at least two different levels over the target as seen along the directions of the respective reference beams.