After formation of a semiconductor device on a semiconductor-on-insulator (SOI) layer, a first dielectric layer is formed over a recessed top surface of a shallow trench isolation structure. A second dielectric layer that can be etched selective to the first dielectric layer is deposited over the first dielectric layer. A contact via hole for a device component located in or on a top semiconductor layer is formed by an etch. During the etch, the second dielectric layer is removed selective to the first dielectric layer, thereby limiting overetch into the first dielectric layer. Due to the etch selectivity, a sufficient amount of the first dielectric layer is present between the bottom of the contact via hole and a bottom semiconductor layer, thus providing electrical isolation for the ETSOI device from the bottom semiconductor layer.