A method for fabricating a semiconductor device is disclosed. An exemplary method includes a providing substrate. A dielectric layer is formed over the semiconductor substrate and a stop layer is formed over the dielectric layer. The stop layer and the dielectric layer comprise a different material. The method further includes forming a patterned hard mask layer over the stop layer and etching the semiconductor substrate through the patterned hard mask layer to form a plurality of trenches. The method also includes depositing an isolation material on the semiconductor substrate and substantially filling the plurality of trenches. Thereafter, performing a CMP process on the semiconductor substrate, wherein the CMP process stops on the stop layer.