Low-temperature electron cyclotron resonance hydrogen plasma cleaning was developed for low-temperature epitaxial growth of Si by ultrahigh vacuum electron cyclotron resonance chemical vapor deposition on oxide-patterned wafers. Defect-free undoped Si epitaxial layers could be obtained by optimizing the hydrogen ion flux and cleaning time, however, in the case of boron-doped Si epitaxial growth, Si epilayers had defect zones away from the bird's beak along the window edges and a defect-free zone at the center of the window. Cross section transmission electron microscopy and energy dispersive spectroscopy results suggest that the defect zone formation is closely related with local oxygen contamination. Possible origins of the local oxygen contamination are discussed.