By investigating the epitaxial growth of Ag(0 0 1) and Au(0 0 1) films and Fe/Ag(0 0 1) and Fe/Au(0 0 1) layered systems on MgO(0 0 1) the influence of carbon contamination of the MgO surface on the morphology of the obtained films is studied. A new technique for the preparation of carbon-free MgO(0 0 1) surfaces using ion beam oxidation is reported. This technique takes advantage of the high chemical activity of dissociated low energy oxygen atoms, which removes the carbon contamination from the MgO surface as confirmed by Auger electron spectroscopy. It is shown that metallic layers grown on carbon-free MgO substrates demonstrate reduced roughness, improved crystallographic quality and enhanced surface magnetic anisotropy compared to those grown on carbon contaminated substrates.