Faceting morphology of Si layers selectively grown at different growth times has been investigated to study facet formation mechanism. The epitaxial layers have been grown on Si(100) patterned substrates using Si2H6 with an ultrahigh vacuum chemical vapor deposition (UHV-CVD) system. It is found that the faceting process consists of two stages. One is the initial stage of faceting, when the faceting planes are generated. In this stage, the faceting morphology changes from (311) faceting to the faceting composed of (311) and (111) planes with increasing layer thickness, because the growth rates of the faceting planes are not constant in these small areas due to the surface Si migration. The morphology transition can be simulated by free energy considerations. After the faceting plane becomes large enough to have a constant growth rate, a second stage follows when the faceting planes have developed due to the difference in growth rate between the (100) plane and each faceting plane.