A method includes providing a substrate having a channel region, forming a gate stack layer over the channel region, forming a patterned hard mask over the gate stack layer, etching a top portion of the gate stack layer through openings in the patterned hard mask with a first etchant, etching a middle portion and a bottom portion of the gate stack layer with a second etchant that includes a passivating gas. A gate stack is formed with a passivation layer deposited on sidewalls of the gate stack. The method also includes etching the gate stack with a third etchant, thereby removing a bottom portion of the passivation layer and recessing a bottom portion of the gate stack.