Si films including hierarchical nanodot structures were developed using ultrathin SiO2 films. Scattering bodies with various size scales are expected to scatter phonons with various wavelengths. This idea is important for reduction of thermal conductivity because phonon, that is boson, with various wavelengths, can contribute to the heat transport. Here, in Si films including Si nanodot structures, the nanodots with various sizes reduced the thermal conductivity effectively in addition to increase of dopant activation rates. Furthermore, highly-doped Si films including Ge nanodots that have atomic scale and nanoscale phonon scattering bodies exhibited drastically-reduced thermal conductivity. This drastic reduction of thermal conductivity came from hierarchical structures that include nanodot structures working as strong phonon scattering bodies. This gives the guideline of control of phonon and carrier transport using nanostructures for high performance thermoelectric materials.