An apparatus includes a first charged particle beam manipulator positioned in a first layer configured to influence a charged particle beam and a second charged particle beam manipulator positioned in a second layer configured to influence the charged particle beam. The first and second charged particle beam manipulators may each include a plurality of electrodes having a first set of opposing electrodes and a second set of opposing electrodes. A first driver system electrically connected to the first set may be configured to provide a plurality of discrete output states to the first set. A second driver system electrically connected to the second set may be configured to provide a plurality of discrete output states to the second set. The first and second charged-particle beam manipulators may each comprise a plurality of segments; and a controller having circuitry configured to individually control operation of each of the plurality of segments.