A method for manufacturing an integrated circuit device includes forming a multi-layer film, such as an ONO film, on a surface of the substrate, the multi-layer film including the first layer of silicon oxide, a middle layer of silicon nitride, and a top layer of silicon oxide. The top layer of silicon oxide has an exposed surface. Next, the process involves exposing the exposed surface of the top layer of the multi-layer film to a plasma containing nitrogen radicals, to form a nitrided layer of oxide on the exposed surface. The nitrided layer of oxide on the top layer of silicon oxide in the multi-layer film has a thickness sufficient to protect the multi-layer film from damage during subsequent cleaning steps, used for example to prepare the substrate for formation of gate oxides in regions remote from the multi-layer film.