A method for forming a shallow trench isolation (STI) structure using two individual STI trench etching processes is provided. A first STI etching process forms first trenches with one or more sizes in rows along a first dimension in a silicon substrate. A first dielectric is filled in the first trenches following a first thermal oxidation forming a first liner oxide surrounding the first trenches. A second STI trench etching process forms second trenches with one or more sizes in a second dimension to define active regions separated from each other by the first trenches filled with the first dielectric material and second trenches. A second dielectric is filled in the second trenches following a second thermal oxidation forming a second liner oxide surrounding the second trenches. Active region encroachment caused by the first and second thermal oxidation is reduced by doing the two individual STI trench etching processes.