In a method of manufacturing a semiconductor device, a first trench is formed in a first region of a substrate and a second trench is formed in a second region of the substrate different from the first region. A depth of the first trench is less than that of the second trench. An insulation layer is formed in the second trench, so that semiconductor structures in the first trench are electrically isolated, and a conductive layer fills the first trench and extends above the first trench.