A method for processing a substrate includes forming a patterned layer over the substrate, the layer including an opening, where a surface of the opening includes a sidewall and a bottom wall. The method includes processing the patterned layer with an anisotropic process by generating a flux of gas clusters over the substrate in a first process chamber, where the gas clusters include radical precursors; exposing the substrate to the flux of gas clusters. The method includes sustaining plasma including ions in a second process chamber; and exposing the substrate to the ions by directing the ions toward the bottom wall of the opening.