A multi-beamlet charged particle beamlet lithography system for transferring a pattern to a surface of a substrate. The system comprises a projection system (311) for projecting a plurality of charged particle beamlets (7) onto the surface of the substrate; a chuck (313) moveable with respect to the projection system; a beamlet measurement sensor (i.a. 505, 511) for determining one or more characteristics of one or more of the charged particle beamlets, the beamlet measurement sensor having a surface (501) for receiving one or more of the charged particle beamlets; and a position mark measurement system for measuring a position of a position mark (610, 620, 635), the position mark measurement system comprising an alignment sensor (361, 362). The chuck comprises a substrate support portion for supporting the substrate, a beamlet measurement sensor portion (460) for accommodating the surface of the beamlet measurement sensor, and a position mark portion (470) for accommodating the position mark.