Method of eliminating micro-trenches during spacer etch

A method of forming a semiconductor structure is provided. The method includes providing a semiconductor substrate with a substrate region. The method also includes forming a pad oxide layer overlying the substrate region. The method additionally includes forming a stop layer overlying the pad oxide layer. Furthermore, the method includes patterning the stop layer and the pad oxide layer to expose a portion of the substrate region. In addition, the method includes forming a trench within an exposed portion of the substrate region, the trench having sidewalls and a bottom and a height. Also, the method includes depositing alternating layers of oxide and silicon nitride to at least fill the trench, the oxide being deposited by an HDP-CVD process. The method additionally includes performing a planarization process to remove a portion of the silicon nitride and oxide layers. In addition, the method includes removing the pad oxide and stop layers.