A method of forming a shallow trench isolation (STI) structure in a substrate includes forming a pad oxide layer over the substrate. The method includes forming a nitride-containing layer over the pad oxide layer, wherein the nitride-containing layer has a first thickness. The method further includes forming the STI structure extending through the nitride-containing layer, into the substrate. The STI structure has a height above a top surface of the pad oxide layer. The method includes establishing a correlation between the first thickness, the height of the STI structure above the top surface of the pad oxide layer, and an offset between the first thickness and the height of the STI structure above the top surface of the pad oxide layer. The method includes calculating the height of the STI structure above the pad oxide layer based on the correlation, and selectively removing a determined thickness of the STI structure.