Isolation regions for semiconductor substrates include dielectric-filled trenches and field oxide regions. Protective caps of dielectric materials dissimilar from the dielectric materials in the main portions of the trenches and field oxide regions may be used to protect the structures from erosion during later process steps. The top surfaces of the isolation structures are coplanar with the surface of the substrate. Field doping regions may be formed beneath the field oxide regions. To meet the demands of different devices, the isolation structures may have varying widths and depths.