A method for controlling a multi-stage system includes a stator extending parallel to a first direction; a first and second stage that are moveable relative to the stator; the stages being provided with a magnet system to generate a magnetic field, and the stator being provided with coils to interact with the magnetic fields to position the stages relative to the stator, the method including: determining the position of the stages; selecting a first and a second subset of coils that are capable of having a non-negligible interaction with the magnetic field of respectively the first and the second stage; activating the coils of both subsets, wherein activating the coils includes determining the coils that are part of both subsets; and excluding a coil that is part of both subsets from activating.