Atomic hydrogen is shown to be particularly efficacious for the preparation of substrates for subsequent growth of II-VI compounds by molecular beam epitaxy. A commercial thermal cracker was used to produce atomic hydrogen in the molecular beam epitaxy growth chamber for in-situ cleaning. This paper discusses the use of atomic hydrogen for both oxide removal from GaAs prior to ZnSe and CdTe growth, and for low-temperature oxide removal from CdTe and HgCdTe. Reflection high energy electron diffraction, ultra violet fluorescence microscopy, Nomarski interference contrast microscopy, and atomic force microscopy were used to characterize the growths.