In a method, a mask is formed on a microstructure over a substrate. The mask includes a first pattern over a first region of the microstructure and a second pattern over a second region of the microstructure. A first etching process is performed to etch the microstructure by providing an etching gas and applying a first bias voltage to the substrate according to the first and second patterns of the mask. A protective layer is subsequently formed by providing a deposition gas and applying a second bias voltage to the substrate to cover the first pattern of the mask. A second etching process is performed to transfer the second pattern of the mask further into the second region of the microstructure. The deposition gas has a higher carbon to fluorine ratio than the etching gas, and the second bias voltage is smaller than the first bias voltage.