Methods and systems for, in one embodiment, accelerating a stage through a clearance height in a first direction and decelerating the stage in the first direction while accelerating in a second direction are shown. The stage is moved in a third direction and a determination is made whether the stage movement in the second direction is below a threshold value before continuing to move the stage further in the third direction. The first direction is perpendicular to the second direction and is parallel and opposite to the third direction.