Abstract: A vacuum chuck system may include a vacuum chuck and a vacuum stopper collection and dispensing system. The vacuum chuck may include a ceramic plate with a retaining surface. The retaining surface may include a plurality of depressions and a plurality of openings, each of the openings being disposed on a bottom surface of one of the depressions and fluidly coupled to a vacuum pump. Vacuum stoppers may be used to seal one or more of the openings so as to restrict the vacuum area of the vacuum chuck. The vacuum stopper collection and dispensing system may be used to collect vacuum stoppers from and dispense vacuum stoppers onto the retaining surface. In addition or in the alternative, an electromagnet or a robotic arm may be used to move a vacuum stopper from a blocking position to a non-blocking position on the retaining surface.