A method of patterning a semiconductor device is disclosed. A tri-layer photoresist is formed over a plurality of patterned features. The tri-layer photoresist includes a bottom layer, a middle layer disposed over the bottom layer, and a top layer disposed over the middle layer, the top layer containing a photo-sensitive material. The top layer is patterned via a photolithography process, the patterned top layer including an opening. The opening is extended into the bottom layer by etching the bottom layer and continuously forming a protective layer on etched surfaces of the bottom layer and on exposed surfaces of the patterned features. The bottom layer is removed. At least some portions of the protective layer remain on the exposed surfaces of the patterned features after the bottom layer is removed.