[Granted] A method of patterning a substrate includes providing a focusing plate adjacent to a plasma chamber containing a plasma, the focusing plate configured to extract ions from the plasma through at least one aperture that provides focused ions towards the substrate. The method further includes directing first ions through the at least one aperture to one or more first regions of the substrate so as to condense first gaseous species provided in ambient of the substrate on the one or more first regions of the substrate.