The use of two different materials for shallow trench isolation and deep structural trenches with a dielectric material therein (e.g., flowable oxide and a HARP oxide, respectively) causes non-uniform heights of exposed portions of raised semiconductor structures for non-planar semiconductor devices, due to the different etch rates of the materials. Non-uniform openings adjacent the exposed portions of the raised structures from recessing the isolation and dielectric materials are filled with additional dielectric material to create a uniform top layer of one material (the dielectric material), which can then be uniformly recessed to expose uniform portions of the raised structures.