Plasma-enhanced chemical vapor deposition (PECVD) is a versatile technique for growing well-aligned, precisely patterned, multiwalled carbon nanotubes directly on substrates. We report on the characterization of PECVD deposited nanotubes using Auger Electron Spectroscopy (AES); we believe that this is the first comprehensive AES study of nanotubes and the effect of the deposition process on the substrate. The nanotubes contained well-crystallized graphitic carbon, in contrast to the amorphous/disordered carbon byproduct which is condensed on the substrate surface. By adjusting the deposition gas ratios, we show, using depth-profiled composition analysis, that it is possible to eliminate the unwanted amorphous carbon on the substrate surface. However, a 5 nm interfacial layer, which contained the plasma species, was always present on the substrate surface due to its exposure to the plasma. We could prevent the formation of this interfacial layer by shielding areas of the substrate from the plasma to achieve truly byproduct free deposition. This technique has allowed us to fabricate promising microelectronic field emission devices using vertically aligned carbon nanotubes.