A Raman probe is used to detect crystal structure of a substrate undergoing thermal processing in a thermal processing system. The Raman probe may be coupled to a targeting system of a laser thermal processing system. The Raman probe includes a laser positioned to direct probe radiation through the targeting system to the substrate, a receiver attuned to Raman radiation emitted by the substrate, and a filter that blocks laser radiation reflected by the substrate. The Raman probe may include more than one laser, more than one receiver, and more than one filter. The Raman probe may provide more than one wavelength of incident radiation to probe the substrate at different depths.