A system for treating substrates, provided with at least one processing chamber to treat at least one substrate with a vacuum process, wherein said processing chamber is provided with a substrate access closable by a closing body, wherein the system is provided with a conveying device which is at least arranged to move said closing body, wherein said conveying device is arranged to convey a mask, intended to at least partly cover said substrate during said vacuum process, at least between a position outside the processing chamber and a position inside the processing chamber. It is advantageous when at least said substrate holder is provided with positioning means to position the substrate holder and the mask relative to each other. The invention further provides a use of such a system.