A method for treating a structure is described. One embodiment includes forming a structure on a substrate, wherein the structure has a plurality of surfaces including one or more first surfaces lying substantially parallel to a first plane parallel with said substrate and one or more second surfaces lying substantially perpendicular to the first plane. Additionally, the method comprises directing a gas cluster ion beam (GCIB) formed from a material source toward the substrate with a direction of incidence, and orienting the substrate relative to the direction of incidence. The method further comprises treating the one or more second surfaces.