Vertically aligned multi walled carbon nanotubes (MWNTs) were synthesized by electron cyclotron resonance chemical vapor deposition on Ni-coated glass substrates at temperatures as low as 400degreesC. Negative self-biases were applied to the substrates by radio-frequency (RF) plasma for ion bombardment of the growing surface. It was observed that ion bombardment by RF biasing to the substrates had a great effect upon the growth of carbon nanotubes and their morphologies. High-resolution transmission electron microscopy revealed that the degree of ordering of graphene layers in the synthesized nanotubes increased with RF bias. Raman spectroscopic analyses indicated that the shortening of C-C bonds within the graphene layers of the MWNTs occurred at larger negative biases, which seemed to result from removal of bonded hydrogen from the MWNTs by ion bombardment.