Methods for selectively oxidizing a semiconductor structure include generating a gas cluster ion beam comprising an oxidizing source gas, directing the gas cluster ion beam to a region of a substrate adjacent a conductive line and exposing the region to the gas cluster ion beam including an oxidizing matter. Utilizing the gas cluster ion beam enables selective oxidation of a targeted region at temperatures substantially lower than those of typical oxidation processes thus, reducing or eliminating oxidation of the conductive line. Semiconductor devices including transistors formed using such methods are also disclosed.