While embedded silicon germanium alloy and silicon carbon alloy provide many useful applications, especially for enhancing the mobility of MOSFETs through stress engineering, formation of alloyed silicide on these surfaces degrades device performance. The present invention provides structures and methods for providing unalloyed silicide on such silicon alloy surfaces placed on semiconductor substrates. This enables the formation of low resistance contacts for both mobility enhanced PFETs with embedded SiGe and mobility enhanced NFETs with embedded Si:C on the same semiconductor substrate. Furthermore, this invention provides methods for thick epitaxial silicon alloy, especially thick epitaxial Si:C alloy, above the level of the gate dielectric to increase the stress on the channel on the transistor devices.