A method of forming a shallow trench isolation layer in a semiconductor device is provided, wherein a first trench and a second trench are formed in an area selected from a semiconductor substrate and a sidewall oxide layer, an anti-oxidation liner, and a mask layer are formed on the semiconductor substrate including the inner surfaces of the first and second trenches, in the same order. Using photoresist lithography, the mask layer and the anti-oxidation layer are etched in the second trench. An isolation layer is formed in the first and second trenches by depositing and then chemically and mechanically polishing the dielectric material and the layers underneath until the semiconductor substrate surface is exposed. The first trench provides isolation between N-FETs, an N-FET and a P-FET, an N-FET and other circuit devices, a P-FET and other circuit devices, and other circuit devices and the second trench provides isolation between P-FETs.