A method of precleaning a substrate includes supporting a substrate with silicon oxide on its surface within a reaction chamber of a semiconductor processing system and flowing a halogen-containing reactant and a hydrogen-containing reactant into the reaction chamber. A first preclean material is formed from the halogen-containing reactant, the hydrogen-containing reactant, and a first portion of the silicon oxide on the surface of the substrate. Additional halogen-containing reactant is flowed into the reaction chamber without flowing additional hydrogen-containing reactant into the reaction chamber, and a second preclean material is formed from the additional halogen-containing reactant and a second portion of the silicon oxide on the surface of the substrate. Methods of forming structures on substrates and semiconductor processing systems are also described.