A method of fabricating a semiconductor device structure is provided. The method begins by providing a substrate having a layer of semiconductor material, a pad oxide layer overlying the layer of semiconductor material, and a pad nitride layer overlying the pad oxide layer. The method proceeds by selectively removing a portion of the pad nitride layer, a portion of the pad oxide layer, and a portion of the layer of semiconductor material to form an isolation trench. Then, the isolation trench is filled with a lower layer of isolation material, a layer of etch stop material, and an upper layer of isolation material, such that the layer of etch stop material is located between the lower layer of isolation material and the upper layer of isolation material. The layer of etch stop material protects the underlying isolation material during subsequent fabrication steps.