A modified STI process is provided comprising forming a first polysilicon layer over a substrate. Forming a trench through the first polysilicon layer and into the substrate, and filling the trench with an oxide layer. Depositing a second polysilicon layer over the oxide, such that the bottom of the second polysilicon layer within the trench is above the bottom of the first polysilicon layer, and the top of the second polysilicon layer within the trench is below the top of the first polysilicon layer. The resulting structure may then be planarized using a CMP process. An alignment key may be formed by selectively etching the oxide layer. A third polysilicon layer may then be deposited and patterned using photoresist to form a gate structure. During patterning, exposed second polysilicon layer is etched. An etch stop is detected at the completion of removal of the second polysilicon layer. A thin layer of the first polysilicon layer remains, to be carefully removed using a subsequent selective etch process.