A method of manufacturing a semiconductor device includes forming a first plurality of recessed regions in a substrate, the substrate having a protruded active region between the first plurality of recessed regions and the protruded active region having an upper surface and a sidewall, forming a device isolation film in the first plurality of recessed regions, the device isolation film exposing the upper surface and an upper portion of the sidewall of the protruded active region, and performing a first plasma treatment on the exposed surface of the protruded active region, wherein the plasma treatment is performed using a plasma gas containing at least one of an inert gas and a hydrogen gas in a temperature of less than or equal to about 700° C.