A semiconductor substrate having an isolation region and method of forming the same. The method includes the steps of providing a substrate having a substrate layer, a buried oxide (BOX), a silicon on insulator (SOI) layer, a pad oxide layer, and a pad nitride layer, forming a shallow trench region, etching the pad oxide layer to form ears and etching the BOX layer to form undercuts, depositing a liner on the shallow trench region, depositing a soft mask over the surface of the shallow trench region, filling the shallow trench region, etching the soft mask so that it is recessed to the top of the BOX layer, etching the liner off certain regions, removing the soft mask, and filling and polishing the shallow trench region. The liner prevents shorting of the semiconductor device when the contacts are misaligned.