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Thermal processing is performed by transmission of mid infra-red laser light through a substrate such as a semiconductor substrate with a limited mid infra-red transmission range. The laser light is generated by a rare-earth-doped fiber laser and is directed through the substrate such that the transmitted power is capable of altering a target material at a back side region of the substrate, for example, on or spaced from the substrate. The substrate may be sufficiently transparent to allow the transmitted mid infra-red laser light to alter the target material without altering the material of the substrate. In one example, the rare-earth-doped fiber laser is a high average power thulium fiber laser operating in a continuous wave (CW) mode and in a 2 µm spectral region.