A differentially pumped deposition system is described that includes a deposition source, such as a magnetron sputtering source, that is positioned in a first chamber. The deposition source generates deposition flux comprising neutral atoms and molecules. A shield that defines an aperture is positioned in the path of the deposition flux. The shield passes the deposition flux though the aperture and substantially blocks the deposition flux from propagating past the shield everywhere else. A substrate support is positioned in the second chamber adjacent to the shield. The pressure in the second chamber is lower than a pressure in the first chamber. A dual-scanning system scans the substrate support relative to the aperture with a first and a second motion, thereby improving uniformity of the deposited thin fill.