A semiconductor device with a deep trench has a dielectric liner formed on sidewalls and a bottom of the deep trench. A pre-etch deposition step of a two-step process forms a protective polymer on an existing top surface of the semiconductor device, and on the dielectric liner proximate to a top surface of the substrate. The pre-etch deposition step does not remove a significant amount of the dielectric liner from the bottom of the deep trench. A main etch step of the two-step process removes the dielectric liner at the bottom of the deep trench while maintaining the protective polymer at the top of the deep trench. The protective polymer is subsequently removed.