Carbon nanotubes are formed on a surface of a substrate using a plasma chemical deposition process. After the nanotubes have been grown, a post-treatment step is performed on the newly formed nanotube structures. The post-treatment removes graphite and other carbon particles from the walls of the grown nanotubes and controls the thickness of the nanotube layer. The post-treatment is performed with the plasma at the same substrate temperature. For the post-treatment, the hydrogen containing gas is used as a plasma source gas. During the transition from the nanotube growth stop to the post treatment step, the pressure in the plasma process chamber is stabilized with the aforementioned purifying gas without shutting off the plasma in the chamber. This eliminates the need to purge and evacuate the plasma process chamber.