Processes for forming isolation structures for semiconductor devices include forming a submerged floor isolation region and a filed trench which together enclose an isolated pocket of the substrate. One process aligns the trench to the floor isolation region. In another process a second, narrower trench is formed in the isolated pocket and filled with a dielectric material while the dielectric material is deposited so as to line the walls and floor of the first trench. The substrate does not contain an epitaxial layer, thereby overcoming the many problems associated with fabricating the same.