A grid plate encoder based positioning system (1) for positioning of an element is provided, the positioning system (1) comprises a grid plate (2) with a grid plate surface (21); an encoder unit (3) with one or more optical sensors (31) for sensing a grid plate surface pattern (23) of the grid plate surface (21); an input (7) to receive coordinates (Xd, Yd) specifying a desired position of the element; a mapping unit (8) to compute compensated coordinate data (Xa, Ya) corresponding to estimated position data expected from the encoder unit (3) when the element is positioned at a desired position (Xd, Yd) specified by the setpoint coordinates; a feedback control unit (9) providing the compensated coordinate data (Xa, Ya) as a setpoint (Xs, Ys) to a positioning unit (12), with feedback control based on the estimated position data obtained from the encoder unit.

Additionally, a grid plate encoder based positioning method and a method for computing compensation data are provided.