The efficiency of thermoelectric devices is based on thermoelectric figure of merit, which can be enhanced by increasing electrical conductivity and lowering thermal conductivity. Thus, semiconductor nanostructures, whose electrical and thermal conductivities could be optimized by changing electronic and structural properties, are ideal candidates for such device applications. However, complete understanding of nanostroctured thermoelectric device properties and limitations requires a technique allowing temperature measurements with nanoscale spatial resolution. In this work, thermal conductivities of Si/SiGe two- and three-dimensional multilayer samples prepared by molecular beam epitaxy (MBE) using Stranski-Krastanov (S-K) growth mode are studied. Sample temperatures during irradiation by a laser beam are measured using Stokes and Anti-Stokes modes of Raman scattering. We find surprising correlations between SiGe cluster vertical self-organization, studied by low frequency Raman spectroscopy and their thermal conductivity. This work suggests a novel approach toward high-efficiency Si/SiGe nanostrocture-based thermoelectric generators.