A method of fabricating a semiconductor device is provided. The method can include forming a hard mask film including lower and upper hard mask films on a substrate in which an active region and an isolation region are defined and patterning the hard mask film to provide a hard mask pattern partially exposing the active region and the isolation region. An etchant can be applied to the active and isolation regions using the hard mask pattern as an etching mask to form a trench in the active region of the substrate while avoiding substantially etching the isolation region exposed to the etchant and a gate can be formed on the trench.