A method is provided for creating a plurality of substantially uniform nano-scale features in a substantially parallel manner in which an array of micro-lenses is positioned on a surface of a substrate, where each micro-lens includes a hole such that the bottom of the hole corresponds to a portion of the surface of the substrate. A flux of charged particles, e.g., a beam of positive ions of a selected element, is applied to the micro-lens array. The flux of charged particles is focused at selected focal points on the substrate surface at the bottoms of the holes of the micro-lens array. The substrate is tilted at one or more selected angles to displace the locations of the focal points across the substrate surface. By depositing material or etching the surface of the substrate, several substantially uniform nanometer sized features may be rapidly created in each hole on the surface of the substrate in a substantially parallel manner.