The goal of this research is to investigate atomic structures, defects, vacancies, and chemical reactions on surfaces induced by atoms/ionss with thermal energies up to several hundred eV as a function of ion kinetic energy and substrate temperature. Thermal atomic beams are produced by effusion cells while ion beams are generated by a new pulsed, mass-selected, low-energy ion beam system. In situ structural analysis are conducted by Time-Of- Flight Scattering and Recoiling Spectrometry and Low Energy Electron Diffraction. In situ X-ray and UV photoelectron and Auger spectroscopy (PS, UPS and AES) and conventional ex situ structural analysis methods such as x-ray diffraction, Rutherford backscattering, and transmission electron microscopy also are used for material characterization. Studies on ion trajectory simulations and molecular dynamics calculations augment structural determinations and atomic scale processes in film growth. These studies are important because they enhance understanding of the fundamental physical and chemical processes involved in low-energy ion-surface interactions. Also, the proposed synthetic routes have potentials for growing unique, previously unknown materials because of the judicious manipulation of the ion energy and substrate temperature.