The effect of HF vapor pre-treatment prior to Co deposition on the sheet resistance of cobalt silicide and gate oxide integrity has been investigated. During the HF cleaning, it was found that a significant amount of fluorine (F) atoms was diffused toward the polycrystalline silicon substrate with a large amount of segregation near the surface. Presence of F at the surface retarded interaction between Co and Si, hence formed non-uniform cobalt silicide. A low-energy sputter cleaning after HF vapor treatment successfully removed the F segregated layer and uniform cobalt silicide was achievable. In addition, gate oxide integrity such as charge-to-break down and leakage current was improved because the pre-existing F atoms block the diffusion of Co and stabilize the gate oxide.