A novel approach for improving the thermal and dimensional stability of a polymer based separator is investigated. The surface of the micropores in the polyolefin based separator is fully covered by a thin layer of SiO2 deposited by the chemical vapor deposition method. Through this new process, the thermal and dimensional stability of the microporous separators is greatly enhanced, thus allowing the commercialization of polymer based separators for large sized battery systems. The morphology of the modified separators as a function of the thickness of the inorganic layer is considered to be a key factor for the optimization of their thermal and dimensional stability without sacrificing their ionic conductivity for the sake of the cell performance. At the optimum thickness of the thin and conformal layer of SiO2, we obtain a polymer separator which is highly stable at high temperature, even above the melting point of the polymer membrane, with satisfactory cell performance, such as its ion conductivity, C-rate and cycle life.