We prepared multilayers of semiconducting half-heusler β-Zn4Sb3 and skutterudites CeFe(4-x)CoxSb12 compound thin films by ion beam assisted deposition (IBAD) system for the application of thermoelectric (TE) materials. Rutherford backscattering spectrometry (RBS) was used to analyze the composition of thin films. The thin films were then bombarded by 5 MeV Si ions for generation of nanodots in the films. We measured the cross-plane thermal conductivity by a house developed 3ω-method system, cross-plane Seebeck coefficient by a (MMR) Seebeck system, and cross plane electrical conductivity of these nanolayered systems by a (MMR) Hall system before and after bombardment. Both β-Zn4Sb3 and CeFe(4-x)CoxSb12 systems have been identified as promising thermoelectric materials for the application of thermal-to-electrical energy conversion. The nanodots produced by MeV ion beam can cause significant change in both electrical and thermal conductivity of thin films, thus improving the efficiency. The MeV ion-beam bombardment resulted in decrease in the thermal conductivity of thin films and increase in the efficiency of thermal-to-electrical energy conversion.