A method and system for controlling a position of a moveable stage having a substrate supported thereon is provided. First position information representing a position of the substrate relative to a mark on an object is obtained from a sensor. Alignment prediction information is generated based on the obtained first position wherein the generated alignment prediction information including at least one parameter value. First trajectory information is generated and includes the at least one parameter value based on the obtained first position information and the generated alignment prediction information. Second trajectory information is generated based on the generated alignment prediction information first trajectory information and second position information, wherein the second position information represents a position of the moveable stage. An output control signal is generated based on the second trajectory information and used to control the moveable stage to approach a target position based on the generated output signal.