A method includes forming a patterned mask comprised of a polish stop layer positioned above a protection layer above a substrate, performing at least one etching process through the patterned mask layer on the substrate to define a trench in the substrate, and forming a layer of silicon dioxide above the patterned mask layer such that the layer of silicon dioxide overfills the trench. The method also includes removing portions of the layer of silicon dioxide positioned outside of the trench to define an isolation structure, performing a dry, selective chemical oxide etching process that removes silicon dioxide selectively relative to the material of the polish stop layer to reduce an overall height of the isolation structure, and performing a selective wet etching process to remove the polish stop layer selectively relative to the isolation region.