A charged particle lithography system for transferring a pattern onto the surface of a target, comprising a beam generator for generating a plurality of charged particle beamlets, the plurality of beamlets defining a column, and a plurality of aperture array elements comprising a first aperture array, a blanker array, a beam stop array, and a projection lens array. Each aperture array element comprises a plurality of apertures arranged in a plurality of groups, the apertures for letting the beamlets pass through the aperture array element, wherein the groups of apertures of each aperture array element form beam areas distinct and separate from a plurality of non-beam areas formed between the beam areas and containing no apertures for passage of the beamlets, and wherein the beam areas of the aperture array elements are aligned to form beam shafts, each comprising a plurality of beamlets, and the non-beam areas of the aperture array elements are aligned to form non-beam shafts not having beamlets present therein. The first aperture array element is provided with cooling channels adapted for transmission of a cooling medium for cooling the first aperture array element, the cooling channels being provided in the non-beam areas of the first aperture array element.