According to one embodiment, a method of manufacturing a semiconductor device, the method includes forming a pillar on a base layer, forming a insulating layer on the base layer to cover the pillar by using GCIB method, where a lowermost portion of an upper surface of the insulating layer is lower than an upper surface of the pillar, and polishing the insulating layer and the pillar to expose a head of the pillar by using CMP method, where an end point of the polishing is the lowermost portion of the upper surface of the insulating layer.