In one embodiment, a method of manufacturing a semiconductor device includes forming a conductive film whose upper surface and side surface are exposed and an insulation film whose upper surface is exposed, on a semiconductor substrate. The method further includes supplying oxidizing ions or nitriding ions contained in plasma generated by a microwave, a radio-frequency wave, or electron cyclotron resonance to the exposed side surface of the conductive film and the exposed upper surface of the insulation film, by applying a predetermined voltage to the semiconductor substrate, thereby performing anisotropic oxidation or anisotropic nitridation of the exposed side surface of the conductive film and the exposed upper surface of the insulation film.