Embodiments of the present invention provide a structure and method for fabrication of deep trenches in semiconductor-on-insulator structures. An upper portion of the deep trench cavity is formed to expose a sidewall of the buried insulator layer. A protective layer is disposed on the sidewall of the buried insulator layer. Then, the cavity is extended into the bulk substrate. The protective layer prevents over etch of the buried insulator layer during this process. The protective layer is then partially removed, such that the semiconductor-on-insulator (SOI) layer sidewall is exposed. The trench is then filled with a conductive fill material, such as polysilicon. The protection of the buried insulator (BOX) layer allows the trenches to be placed closer together while reducing the risk of a short circuit due to over etch, thereby increasing circuit density and product yield.