A method of processing a substrate by omitting a photolithographic process is disclosed. The method includes forming at least one layer on a stepped structure having an upper surface, a lower surface, and a side surface that connects the upper surface to the lower surface, selectively densifying portions of the at least one layer respectively on the upper surface and the lower surface via asymmetric plasma application, and performing an isotropic etching process on the at least one layer. During the isotropic etching process, the portion of the at least one layer formed on the upper surface is separated from the portion of the at least one layer formed on the lower surface.