Nanostructure-based charge storage regions are included in non-volatile memory devices and integrated with the fabrication of select gates and peripheral circuitry. One or more nanostructure coatings are applied over a substrate at a memory array area and a peripheral circuitry area. Various processes for removing the nanostructure coating from undesired areas of the substrate, such as target areas for select gates and peripheral transistors, are provided. One or more nanostructure coatings are formed using self-assembly based processes to selectively form nanostructures over active areas of the substrate in one example. Self-assembly permits the formation of discrete lines of nanostructures that are electrically isolated from one another without requiring patterning or etching of the nanostructure coating.