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We study the effects of phonon boundary scattering on the transport of thermal energy in semiconductor thin films across multiple length scales and temperatures. We use a model based on the kinetic theory of transport processes that accurately calculates the reduction of the phonon mean free paths by including the effects of spatial location and propagation direction of phonons. We investigate how the effective phonon mean free paths and the resultant thermal conductivities are reduced by the film length scale and surface roughness. The thermal conductivities of silicon and germanium thin films are calculated for temperatures between 4 K and 500 K and thicknesses from nano to micro and good agreement is obtained with experimental measurements. The theoretical study in this paper helps to understand and quantitatively predict the transport of thermal energy in nanoscale materials, which can be used to improve the efficiency of optoelectronic devices and thermoelectric materials.