You can use Raman selection rules to remove the signal from the Si substrate, but of course the carbon doped Si film must not have the same crystallographic orientation, else its signal wouldl be eliminated at the same time.

UV could be a solution but it depends on the wavelength. 364 nm is a resonant excitation for crystalline silicon. The signal from the Si substrate could be strongly enhanced if it is not totally absorbed in the carbon doped layer.