According to example embodiments of inventive concepts, a method of fabricating a semiconductor device includes: forming a preliminary stack structure, the preliminary stack structure defining a through hole; forming a protection layer and a dielectric layer in the through hole; forming a channel pattern, a gapfill pattern, and a contact pattern in the through hole; forming an offset oxide on the preliminary stack structure; measuring thickness data of the offset oxide; and scanning the offset oxide using a reactive gas cluster ion beam. The scanning the offset oxide includes setting a scan speed based on the measured thickness data of the offset oxide, and forming a gas cluster.