A method for operating a target processing system for processing a target on a chuck, the method comprising: providing at least a first chuck position mark and a second chuck position mark on the chuck; providing an alignment sensing system comprising at least a first alignment sensor and a second alignment sensor arranged for detecting the first and second chuck position marks (27, 28) respectively; providing a final projection system arranged to project a patterning beam onto the target; providing a chuck position measurement system comprising at least two differential interferometers arranged to measure the position of the chuck with respect to the final projection system of said target processing system; providing a level sensing system comprising a plurality of level sensors (57, 58, 59), and providing a reference surface on the chuck; moving the chuck to a first position based on at least one measurement of the alignment sensing system, said moving the chuck comprising moving the chuck to align the first and second chuck position marks with the first and second alignment sensors and reading the first and second chuck position marks by the first and second alignment sensor; measuring at least one value relating to the orientation of the reference surface with respect to the level sensors, and moving the chuck to align the reference surface with a level sensor plane of the plurality of level sensors, such that in the first position the first and second chuck position marks are aligned with the first and second alignment sensors and the reference surface is aligned with the level sensor plane; measuring at least one value related to the first position of the chuck, comprising measuring an output of each of the differential interferometers; and initializing the interferometers with the chuck located at the first position, based on said measuring of said at least one value related to the first position of the chuck. providing at least a first chuck position mark and a second chuck position mark on the chuck; providing an alignment sensing system comprising at least a first alignment sensor and a second alignment sensor arranged for detecting the first and second chuck position marks (27, 28) respectively; providing a final projection system arranged to project a patterning beam onto the target; providing a chuck position measurement system comprising at least two differential interferometers arranged to measure the position of the chuck with respect to the final projection system of said target processing system; providing a level sensing system comprising a plurality of level sensors (57, 58, 59), and providing a reference surface on the chuck; moving the chuck to a first position based on at least one measurement of the alignment sensing system, said moving the chuck comprising moving the chuck to align the first and second chuck position marks with the first and second alignment sensors and reading the first and second chuck position marks by the first and second alignment sensor; measuring at least one value relating to the orientation of the reference surface with respect to the level sensors, and moving the chuck to align the reference surface with a level sensor plane of the plurality of level sensors, such that in the first position the first and second chuck position marks are aligned with the first and second alignment sensors and the reference surface is aligned with the level sensor plane; measuring at least one value related to the first position of the chuck, comprising measuring an output of each of the differential interferometers; and initializing the interferometers with the chuck located at the first position, based on said measuring of said at least one value related to the first position of the chuck.