A method for operating a target processing system for processing a target (23) on a chuck (13), the method comprising providing at least a first chuck position mark (27) and a second chuck position mark (28) on the chuck (13); providing an alignment sensing system (17) arranged for detecting the first and second chuck position marks (27, 28), the alignment sensing system (17) comprising at least a first alignment sensor (61) and a second alignment sensor (62); moving the chuck (13) to a first position based on at least one measurement of the alignment sensing system (17); and measuring at least one value related to the first position of the chuck.