High energy ion beams are used to modify co-deposited nanolayer films of alternated materials (e.g. insulator and metal, two different semiconductors, even more complex arrangements) to form nanodots through localized nucleation. The particular application being considered here is for high efficiency thermoelectric conversion systems. The performance of a thermoelectric converter is generally given by the figure of merit, ZT, which is a function of the Seebeck coefficient, electrical conductivity, and thermal conductivity. A high performance device would have a maximized electrical conductivity and a minimized thermal conductivity (maximum electron transport, minimal phonon transport). The current models of electron and phonon transportation through 1D, 2D, 3D quantum regimented structures assume an infinitely repetitive perfect structural “cell”, with complicated algorithms requiring intensive computing power. The main focus for this modeling effort is to reduce the three-dimensional problem to a single dimensional approximation without sacrificing the quality of the result. The nanostructure being investigated has Si and Ge quantum dots arranged with perfect periodicity in all three Cartesian directions, with the heat and electricity flow monitored in the z-direction (cross-plane as initially layered). Non-Equilibrium Green’s Functions Formalism (NEGF) is the mode for calculating the theoretical electrical properties assuming a one-dimensional quantum well arrangement in the z-direction (with finite boundaries in the x and y directions) with tight binding (nearest neighbor approximation). The results are to be compared with experimental measurements on such structures.