A method for forming an aperture pattern in a substrate, the substrate including a film disposed thereon and a patterned mask layer disposed on the film, comprises 1) exposing the substrate to a vapor of a passivation molecule in a non-plasma condition for a period to form a surface protective layer on the patterned mask layer, 2) exposing the substrate to a plasma activated etch gas and plasma dry etching the substrate to form apertures over the patterned mask layer in the film with the plasma activated etch gas, and 3) repeating step 1) and 2) until a desired aperture pattern is formed in the film, wherein the surface protective layer is also formed on the sidewalls of the apertures formed in the film, wherein the passivation molecule has a boiling point equal to or larger than 20° C.