Combined wet and dry cleaning via hydrofluoric acid (HF) and atomic hydrogen on Si 0.6 Ge 0.4 (001) surface was studied at the atomic level using ultrahigh vacuum scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS), and x-ray photoelectron spectroscopy to understand the chemical transformations of the surface. Aqueous HF removes native oxide, but residual carbon and oxygen are still observed on Si 0.6 Ge 0.4 (001) due to hydrocarbon contamination from post HF exposure to ambient. The oxygen contamination can be eliminated by shielding the sample from ambient via covering the sample in the HF cleaning solution until the sample is introduced to the vacuum chamber or by transferring the sample in an inert environment; however, both processes still leave carbon contaminant. Dry in-situ atomic hydrogen cleaning above 330 C removes the carbon contamination on the surface consistent with a thermally activated atomic hydrogen reaction with surface hydrocarbon. A postdeposition anneal at 550 C induces formation of an atomically flat and ordered SiGe surface observed by STM. STS verifies that the wet and dry cleaned surface has an unpinned Fermi level with no states between the conduction and valence band edge comparable to sputter cleaned SiGe surfaces. V