We have developed a simple process to form epitaxial CoSi2 for shallow junction. Prior to metal deposition, the patterned wafers were treated with HF-vapor passivation. As observed by scanning tunneling microscopy (STM), this HF treatment drastically improves the native oxide-induced surface roughness. The epitaxial behavior was confirmed by cross-sectional transmission electron microscopy (TEM). Decreased sheet resistance and leakage current, and improved thermal stability are displayed by the HF treated samples, which is consistent with STM and TEM results.