Semiconductor devices are provided with encapsulating films for protection of sidewall features during fabrication processes, such as etching to form isolation regions. In a non-volatile flash memory, for example, a trench isolation process is divided into segments to incorporate an encapsulating film along the sidewalls of charge storage material. A pattern is formed over the layer stack followed by etching the charge storage material to form strips elongated in the column direction across the substrate, with a layer of tunnel dielectric material therebetween. Before etching the substrate, an encapsulating film is formed along the sidewalls of the strips of charge storage material. The encapsulating film can protect the sidewalls of the charge storage material during subsequent cleaning, oxidation and etch processes. In another example, the encapsulating film is simultaneously formed while etching to form strips of charge storage material and the isolation trenches.