A sputtering system for depositing a thin film on the surface of a disc substrate in which high precision positioning of an inner mask and an outer mask is facilitated. The sputtering system has a mask member placed on the surface of the substrate mounted on a substrate holder to cover a partial region on the surface of the substrate. A thin film is deposited by sputtering in a region on the surface of the substrate not covered by the mask member. A section for carrying in and carrying out the substrate has mechanically holds and releases the substrate holder mounting the substrate, and mechanically holds and releases the mask member.