In one embodiment, an apparatus to selectively deposit a carbon layer on substrate, comprising a plasma chamber to receive a flow of carbon-containing gas; a power source to generate a plasma containing the carbon-containing gas in the plasma chamber; an extraction plate to extract an ion beam from the plasma and direct the ion beam to the substrate, the ion beam comprising ions having trajectories forming a non-zero angle of incidence with respect to a perpendicular to a plane of the substrate, the extraction plate further configured to conduct a neutral species derived from the carbon-containing gas to the substrate; and a substrate stage facing the extraction plate and including a heater to heat the substrate to a first temperature, when the ion beam and carbon-containing species impinge on the substrate.