A method for determining a commutation offset for a mover (250A) of a mover assembly (220C) that moves and positions a stage (220A) relative to a stage base (220B) includes controlling the mover assembly (220C) in a closed loop fashion to maintain the position of the stage (220A) along a first axis and along a second axis with the stage (220A) levitated above the stage base (220B). The method also includes the steps of (i) directing current to a coil array (240) of the mover assembly (220C) so that the mover assembly (220C) imparts a disturbance on the stage (220A); and (ii) evaluating one or more forces generated by the mover assembly (220C) as a result of the disturbance on the stage (220A) created by the mover (250A). Further, a method for generating a compensation map (1402) includes sequentially directing a plurality of excitation signals to the control of the mover assembly (220C) and determining the control commands that result from the plurality of excitation signals.