Co ion implantation into Si substrate with a metal vapor vacuum are (MEWA) ion source has been studied by spectroscopic ellipsometry (SE) over the wavelength range of 400-2000 nm. A series of samples synthesized at different substrate temperatures during implantation (T-S) and then post-annealed at the same conditions have been investigated. SE studies show that the buried CoSi2 layer shifts towards the surface and the surface roughness becomes thicker as T-S increases. Studies also show that, using MEVVA implantation, buried CoSi2 layers can be formed at relatively low T-S and relatively low annealing temperature. However, higher temperature annealing is essential for elimination of the damage in the top Si layer and formation of sharp interface.