Novel diamond films were deposited from methane-hydrogen mixtures by microwave plasma enhanced chemical vapor deposition. While X-ray diffraction provided the definite evidence for the diamond phase, Raman spectroscopy, scanning electron microscopy, and atomic force microscopy exhibited their defective nature, which consisted of nanocrystalline grains with appreciable amount of sp(2)-bonded carbons at the grain boundaries. For the non-destructive depth profiling of these films, multi-layer modeling of ellipsometric spectra was carried out by using Bruggeman's effective medium approximation; the diamond layers with sp(2)-bonded carbon inclusions were optically represented as mixtures of diamond and glassy carbon. All examined defective diamond films with the thickness ranging from 170 to 430 nm exhibited the identical three-layer structure of an glassy-carbon-rich interface layer, a bulk-like layer, and a surface-roughness layer, regardless of the methane concentration. Even in the case of the thinner film of 57 nm, the similar interface layer was observed. However, in the case of the very thin film, silicon carbide layer was detected.