A material processing system includes a particle beam column for directing a particle beam at a first processing region and a laser scanner for directing a laser beam at a second processing region. A method for operating the material processing system includes: scanning a first mark placed on an object with the particle beam; scanning the first mark with the laser beam for a first time and producing a second mark on the object with the laser beam; scanning the second mark with the particle beam; and scanning the first mark with the laser beam for a second time and removing material of the object with the laser beam based on the scanning of the second mark with the particle beam.