Effects of isolation materials on facet formation for low temperature Si selective epitaxial growth (SEG) using Si2H6 have been demonstrated by ultrahigh vacuum-chemical molecular epitaxy (UHV-CME) system. The activation energy of the Si epitaxial growth is 47.35 Kcal/mol. The isolation material includes silicon nitride, wet oxide, and tetraethylorthosilicate (TEOS) oxide. Different isolation materials have different faceting behaviors for the Si epilayer. A silicon nitride mask and a wet oxide mask result in a preferred faceting plane of (111) and (311), respectively. Using a TEOS oxide mask, we obtain a low temperature Si SEG layer without facet and twin formation. The preferred faceting plane orientation for different isolation materials is ascribed to the difference in the interface free energy between the Si layer and the isolation material.