A wafer-level lens forming method for forming an aperture wafer wherein the aperture wafer is stacked with one or more lens wafers to form apertured lens systems. The aperture wafer is formed by lithographically depositing an opaque layer on a transparent film, which is supported by a substrate. The aperture wafer is stacked with one or more lens wafers, and appropriate spacing between the wafers is set with spacer wafers. The substrate is removed, and the lens and aperture wafers are adhered together in a stack to form an optical system. The method avoids accumulation of residual material on the lens during the opaque-layer deposition process. The resulting optical system benefits from added flexibility of the lens system design due to the ability to locate the aperture with respect to one or more lenses independently of the lens wafers.