A semiconductor apparatus and fabrication method for forming oxide isolation regions in a semiconductor substrate for use in forming self-aligned, floating gate MOS structures or other semiconductor devices. The method includes providing a semiconductor substrate member prefabricated having a barrier oxide layer, a polysilicon layer and a plurality of spaced apart silicon nitride layer portions fabricated on the polysilicon layer. The nitride layer portions delineate regions for forming the self-aligned floating gate MOS structures, as well as delineating portions of the silicon dioxide layer and portions of said polysilicon layer that are unprotected by the plurality of silicon nitride layer portions. The method further includes the step of implanting oxygen O.sub.2 ions into regions of the substrate, including those unprotected portions of the silicon dioxide layer and portions of the polysilicon layer to form the oxide isolation regions. After removing the silicon nitride layer portions, and exposing the polysilicon layer portions, the implanted structure is annealed and made ready for forming the self-aligned floating gate MOS structures, or other semiconductor structure on the conductive material pads. The floating gates may be formed having a minimal width with respect to an underlying active region.