Lithography system for processing a target, such as a wafer, the target comprising a target surface, the lithography system comprising - a beam source arranged for providing a charged particle patterning beam, such as an electron beam, the beam comprising at least two beamlets; - a final projection system arranged for projecting a pattern on the target surface with said patterning beam; - a chuck arranged for supporting the target, wherein the chuck comprises a beam measurement sensor and a chuck surface provided with at least one chuck position mark thereon, the beam measurement sensor being arranged for measuring beam properties of the patterning beam, the beam properties comprising a spatial distribution of an intensity of the patterning beam and/or preferably a spatial distribution of the at least two beamlets; - an actuator system (818, 819) arranged for moving the chuck in at least one dimension with respect to the final projection system; - a chuck position sensor system, arranged for measuring the position of the chuck with respect to the final projection system in chuck position coordinates; and, - a mark position system connected to the final projection system and arranged for detecting a position mark (22; 24; 73) on a surface, such as the at least one chuck position mark on the chuck surface, - a support supporting and connected to the mark position system and the final projection system, wherein the mark position system is connected to the final projection system via said support, - a frame and at least three flexures, wherein the support is suspended from the frame with the at least three flexures, wherein - the beam measurement sensor is further arranged for providing beam properties information based on the measured beam properties of the patterning beam; - the chuck position sensor system is further arranged for providing chuck position information based on a measured position of the chuck; - the mark position system is further arranged for providing mark detection information based on a detected mark (22; 24; 73); and, the lithography system further comprises a processing unit arranged for: - controlling the actuator system (818, 819); - receiving the mark detection information, chuck position information and beam properties information; - determining the position of the at least one chuck position mark in chuck coordinates; - determining a spatial distribution of beam properties in chuck coordinates; and, - determining a spatial distribution of beam properties with respect to the position of the at least one chuck position mark. - a beam source arranged for providing a charged particle patterning beam, such as an electron beam, the beam comprising at least two beamlets; - a final projection system arranged for projecting a pattern on the target surface with said patterning beam; - a chuck arranged for supporting the target, wherein the chuck comprises a beam measurement sensor and a chuck surface provided with at least one chuck position mark thereon, the beam measurement sensor being arranged for measuring beam properties of the patterning beam, the beam properties comprising a spatial distribution of an intensity of the patterning beam and/or preferably a spatial distribution of the at least two beamlets; - an actuator system (818, 819) arranged for moving the chuck in at least one dimension with respect to the final projection system; - a chuck position sensor system, arranged for measuring the position of the chuck with respect to the final projection system in chuck position coordinates; and, - a mark position system connected to the final projection system and arranged for detecting a position mark (22; 24; 73) on a surface, such as the at least one chuck position mark on the chuck surface, - a support supporting and connected to the mark position system and the final projection system, wherein the mark position system is connected to the final projection system via said support, - a frame and at least three flexures, wherein the support is suspended from the frame with the at least three flexures, wherein - the beam measurement sensor is further arranged for providing beam properties information based on the measured beam properties of the patterning beam; - the chuck position sensor system is further arranged for providing chuck position information based on a measured position of the chuck; - the mark position system is further arranged for providing mark detection information based on a detected mark (22; 24; 73); and, - controlling the actuator system (818, 819); - receiving the mark detection information, chuck position information and beam properties information; - determining the position of the at least one chuck position mark in chuck coordinates; - determining a spatial distribution of beam properties in chuck coordinates; and, - determining a spatial distribution of beam properties with respect to the position of the at least one chuck position mark.