Methods and control systems are provided for controlling stage position errors based, in some embodiments, on a selection of frequency components in a stage position error signal. An error frequency representation of a position error signal may be generated in the frequency domain and filtered by selecting one or more desired frequency components. The filtered error frequency representation can then be manipulated according to a control law and transformed back into the time domain to generate a current control signal. The current control signal can then be used to adjust the position of the stage to reduce positioning error.