High-quality semiconductor thin films are the basis for high-performance optoelectronic devices, of which the optoelectronic properties are restricted by the substrates. Experimental evaluation of the substrate beneath the thin films is therefore crucial for optimizing film growth. Unfortunately, such evaluation of substrates is usually severely affected by the capping thin films. This paper reports a Fourier transform (FT) Raman spectroscopic method, which utilizes the deep penetration characteristics of infrared pumping light with low photon energy, reduces the influence of the capping film, and extracts the Raman scattering information of the semiconductor substrate effectively. Application to CdTe thin films on GaAs-substrate demonstrates suppression of the CdTe while enhancement of the GaAs-substrate Raman scattering, as compared to a conventional Raman method. The signal-to-noise ratio of the spectrum exceeds 70, indicating the FT-Raman method a feasible approach for experimentally probing semiconductor substrate beneath thin films and/or multilayer structure.