We made p-type nanoscale super lattice thermoelectric cooling devices which consist of multiple periodic layers of Si1−x Gex / Si, The thickness of each layer ranges between 10 and 50 nm. The super lattice was bombarded by 5 MeV Si ion with different fluencies aiming to form nano-cluster quantum dot structures. We estimated the thermo-electric efficiency of the so fabricated devices, measuring the thin film cross plane thermal conductivity by the 3rd harmonic method, measuring the cross plane Seebeck coefficient, and finally measuring the cross plane electric conductivity before and after ion bombardment. As predicted, the thermo-electric Figure of Merit of the films increases with increasing Si ion fluencies. In addition to the effect of quantum well confinement of the phonon transmission, the nano-scale crystal quantum dots produced by the incident Si beam further adversely affects the thermal conductivity by absorbing and dissipating phonon along the lattice, and therefore further reduces the cross plane thermal conductivity, This process increases the electron density of state therefore increasing Seebeck coefficient, and the electric conductivity.