A particle beam lithography method for imaging a structure pattern onto one or more fields on a substrate (11) by means of electrically charged particles, e.g. ions, in which a particle beam is shaped into a desired beam pattern by means of a mask positioned in the particle beam, converted into a beam pattern by apertures in the mask and projected onto the substrate to form an image of the mask apertures. According to the invention, a plurality of masks is positioned on one mask carrier, thus offering a plurality of aperture patterns which are used for producing structure patterns to be imaged onto respective areas (S) of the substrate. The patterns thus imaged, as a whole, combine together to form e.g. the total pattern of a die-field (D) of the substrate (11). By means of reference marks provided for each mask reference beamlets are produced, projected and measured with respect to their position, and from the measurement, alignment control signals are determined for aligning the position of the imaged pattern with a desired position on the substrate.