An apparatus and method for processing a workpiece with a beam is described. The apparatus includes a vacuum chamber having a beam-line for forming a particle beam and treating a workpiece with the particle beam, and a scanner for translating the workpiece through the particle beam. The apparatus further includes a scanner control circuit coupled to the scanner, and configured to control a scan property of the scanner, and a beam control circuit coupled to at least one beam-line component, and configured to control the beam flux of the particle beam according to a duty cycle for switching between at least two different states during processing.