The present disclosure provides methods and apparatus of fluorine passivation in IC device fabrication. In one embodiment, a method of fabricating a semiconductor device includes providing a substrate and passivating a surface of the substrate with a mixture of hydrofluoric acid and alcohol to form a fluorine-passivated surface. The method further includes forming a gate dielectric layer over the fluorine-passivated surface, and then forming a metal gate electrode over the gate dielectric layer. A semiconductor device fabricated by such a method is also disclosed.