A method and apparatus for controlling deflection, deceleration, and focus of an ion beam are disclosed. The apparatus may include a graded deflection/deceleration lens including a plurality of upper and lower electrodes disposed on opposite sides of an ion beam, as well as a control system for adjusting the voltages applied to the electrodes. The difference in potential between pairs of upper and lower electrodes are varied using a set of “virtual knobs” that are operable to independently control deflection and deceleration of the ion beam. The virtual knobs include control of beam focus and residual energy contamination, control of upstream electron suppression, control of beam deflection, and fine tuning of the final deflection angle of the beam while constraining the beam's position at the exit of the lens. In one embodiment, this is done by fine tuning beam deflection while constraining the beam position at the exit of the VEEF. In another embodiment, this is done by fine tuning beam deflection while measuring the beam position and angle at the wafer plane. In a further embodiment, this is done by tuning a deflection factor to achieve a centered beam at the wafer plane.