The invention forms an 
epitaxial silicon-containing layer on a 
silicon germanium, patterned 
strained silicon, or patterned thin 
silicon-on-insulator surface and avoids creating a 
rough surface upon which the 
epitaxial silicon-containing layer is grown. In order to avoid creating the 
rough surface, the invention first performs a 
hydrofluoric acid etching process on the 
silicon germanium, patterned 
strained silicon, or patterned thin silicon-on-insulator surface. This 
etching process removes most of 
oxide from the surface, and leaves a first amount of 
oxygen (typically 1×1013−1×1015 / cm2 of 
oxygen) on the 
silicon germanium, patterned 
strained silicon, or patterned thin silicon-on-insulator surface. The invention then performs a 
hydrogen pre-bake process which heats the 
silicon germanium, patterned strained silicon, or patterned thin silicon-on-insulator surface sufficiently to remove additional 
oxygen from the surface and leave a second amount of oxygen, less than the first amount, on the 
silicon germanium, patterned strained silicon, or patterned thin silicon-on-insulator surface. The heating process leaves an amount of at least 5×1012 / cm2 of oxygen (typically, between approximately 1×1013 / cm2 and approximately 5×1013 / cm2 of oxygen) on the silicon 
germanium, patterned strained silicon, or patterned thin silicon-on-insulator surface. By leaving a small amount of oxygen on the silicon germanium, patterned strained silicon, or patterned silicon-on-insulator surface, the heating processes avoid changing the roughness of the silicon germanium, patterned strained silicon, or patterned thin silicon-on-insulator surface. Then the process of epitaxially growing the 
epitaxial silicon-containing layer on the silicon germanium, patterned strained silicon, or patterned silicon-on-insulator surface is performed.