Low temperature (50-400 °C) and low pressure (10-300 mTorr) processing conditions for remote H-plasma cleaning of Si(100) substrates were investigated. After plasma exposure, ordered surfaces were obtained which displayed 2×1, 3×1 and 1×1 LEED diffraction patterns. The surface phases following the H-plasma clean were dependent on temperature and pressure. The electronic states of the surfaces were explored with angle resolved uv-photoemission spectroscopy (ARUPS) and states due to Si-H bonding were identified. The atomic interactions at the surface were modeled in terms of several processes including Eley-Rideal abstraction, thermally activated desorption and a physisorbed weakly bound state. The kinetic model was able to describe the transitions observed in the processing results. Suitability of the cleaning process for low temperature epitaxy was demonstrated by low temperature MBE epi-growth on an H-terminated 2×1 surface. The initial oxide formation on the H-terminated surfaces were studied by ARUPS.