An IGFET device isolation structure fabrication scheme includes the formation of electrically insulating isolation structures that extend into the substrate and extend above the surface of the substrate. The isolation structures are formed by providing a first mask to form trenches in the substrate. A layer of silicon dioxide is then deposited, filling the trenches and extending above the surface of the substrate. A second mask layer is formed. The second mask layer shadows the trench regions that were formed in the substrate. The silicon dioxide not shadowed by the second mask layer is removed, leaving isolation structures that extend both into the substrate and which rise above the substrate. A gate structure is formed in the region between two isolation structures, and, in the preferred embodiment, the gate structure extends above the substrate to the same height as the isolation structures. The isolation structures and the gate structure can be used to provide self-aligned doped source/drain regions. Spacers can be added to the isolation structure walls and the gate structure walls to provide heavily-doped self-aligned regions.