Prediction based systems and methods for optimizing wafer chucking and lithography control are disclosed. Distortions predicted to occur when a wafer is chucked by a chucking device are calculated and are utilized to control chucking parameters of the chucking device. Chucking parameters may include chucking pressures and chucking sequences. In addition, predicted distortions may also be utilized to facilitate application of anticipatory corrections. Controlling chucking parameters and/or applying anticipatory corrections help reducing or minimizing overlay errors.