A generic, CMOS compatible strategy for transferring a block copolymer template to a semiconductor substrate is demonstrated. An aluminum oxide (Al(2)O(3)) hard mask is selectively deposited by atomic layer deposition in an organized array of holes obtained in a PS matrix via PS-b-PMMA self-assembly. The Al(2)O(3) nanodots act as a highly resistant mask to plasma etching, and are used to pattern high aspect ratio (>10) silicon nanowires and nanopillars.