One embodiment of the present invention provides a process for selective etching during semiconductor manufacturing. The process starts by receiving a silicon substrate with a first layer composed of a first material, which is covered by a second layer composed of a second material. The process then performs a first etching operation that etches some but not all of the second layer, so that a portion of the second layer remains covering the first layer. Next, the system performs a second etching operation to selectively etch through the remaining portion of the second layer using a selective etchant. The etch rate of the selective etchant through the second material is faster than an etch rate of the selective etchant through the first material, so that the second etching operation etches through the remaining portion of the second layer and stops at the first layer.