A charged particle lithography system for transferring a pattern onto the surface of a target. The system comprises a beam generator for generating a plurality of charged particle beamlets, the plurality of beamlets defining a column, a beam stop array having a surface for blocking beamlets from reaching the target surface and an array of apertures in the surface for allowing the beamlets to reach the target surface, and a modulation device for modulating the beamlets to prevent one or more of the beamlets from reaching the target surface or allow one or more of the beamlets to reach the target surface, by deflecting or not deflecting the beamlets so that the beamlets are blocked or not blocked by the beam stop array.