A method for fabricating a layer structure in a trench includes: simultaneously forming a dielectric film containing a Si—N bond on an upper surface, and a bottom surface and sidewalls of the trench, wherein a top/bottom portion of the film formed on the upper surface and the bottom surface and a sidewall portion of the film formed on the sidewalls are given different chemical resistance properties by bombardment of a plasma excited by applying voltage between two electrodes between which the substrate is place in parallel to the two electrodes; and substantially removing either one of but not both of the top/bottom portion and the sidewall portion of the film by wet etching which removes the one of the top/bottom portion and the sidewall portion of the film more predominantly than the other according to the different chemical resistance properties.