A method of fabricating a semiconductor device is provided. The method of fabricating the semiconductor device comprises providing a substrate. Next, an insulating layer, a conductive layer and a silicide layer are formed on the substrate in sequence. Next, a hard masking layer is formed on the silicide layer exposing a portion of the silicide layer. A first etching step is performed to remove the silicide layer and the underlying conductive layer which are not covered by the hard masking layer, thereby forming a gate stack. And next, a second etching step is performed to remove any remaining conductive layer not covered by the hard masking layer after the first etching step. The second etching step is performed with an etchant comprising ammonium hydroxide.