Low temperature processing, which includes in-situ cleaning and epitaxial deposition, is not only important for future silicon ULSI (Ultra Large Scale Integration) technology but also for silicon based heterostructures. Low temperature processing cannot volatilize or dissolve the surface contaminants by heating the substrate, as was accomplished in the traditional high temperature epitaxial growth. In this study, electron cyclotron resonance (ECR) hydrogen plasma was used and films were deposited thermally at a low temperature. The epitaxial films, which were deposited in our chemical vapor deposition systems, immediately after the insitu cleaning processes were characterized by cross-sectional transmission electron microscopy, etc. The role of a hydrogen ion in the in-situ cleaning was clarified by investigating the cleaning efficiencies for a variety of conditions. Process variables such as cleaning temperature and d.c. bias were investigated, and the d.c bias turned out to play a crucial role in low-temperature in-situ cleaning processes. Also, the effect of the in-situ cleaning temperature on the cleaning efficiency was investigated and discussed.