A method of fabricating a semiconductor device according to one embodiment includes: forming a plurality of Si-based pattern portions above a semiconductor substrate, the plurality of Si-based pattern portions being adjacent in a direction substantially parallel to a surface of the semiconductor substrate via insulating films; forming a metal film above the plurality of Si-based pattern portions and the insulating films so as to contact with the plurality of Si-based pattern portions; processing whole areas or upper portions of the plurality of Si-based pattern portions into a plurality of silicide layers by a silicidation reaction between the plurality of Si-based pattern portions and the metal film by heat treatment; and removing the plurality of silicide layers formed above the insulating films by applying planarizing treatment to the plurality of silicide layers.