In order to utilise the full potential of carbon nanotubes/nanofibers, it is necessary to be able to synthesize well aligned nanotubes/nanofibres at desired locations on a substrate. This paper examines the preferential growth of aligned carbon nanofibres by PECVD using lithographically patterned catalysts. In the PECVD deposition process, amorphous carbon is deposited together with the nanotubes due to the plasma decomposition of the carbon feed gas, in this case, acetylene. The challenge is to uniformly nucleate nanotubes and reduce the unwanted amorphous carbon on both the patterned and unpatterned areas. An etching gas (ammonia) is thus also incorporated into the PECVD process and by appropriately balancing the acetylene to ammonia ratio, conditions are obtained where no unwanted amorphous carbon is deposited. In this paper, we demonstrate high yield, uniform, ‘clean’ and preferential growth of vertically aligned nanotubes using PECVD.