A method of manufacturing a semiconductor structure includes forming a lower hard mask layer on a substrate. A patterned middle hard mask layer is formed on the lower hard mask layer, and the patterned middle hard mask layer has a plurality of openings exposing a portion of the lower hard mask layer. A patterned lower hard mask layer and a textured substrate having a plurality of trenches are formed by etching the exposed portion of the lower hard mask layer and a portion of the substrate under the exposed portion of the lower hard mask layer. A steam treatment is then performed on the textured substrate having the trenchess. An isolation oxide layer is formed to fill the trenches.