Aligned carbon nanotubes (CNTs)/carbon nanofibers (CNFs) are synthesized at temperatures of 350, 400 and 450 A degrees C using pulsed plasma enhanced chemical vapour deposition (Pulsed-PECVD) process. Ni catalyst film of thickness 10 nm is directly deposited on molybdenum (Mo) substrate and growth of CNT is performed at various temperatures. Pulsed-PECVD facilitates aligned CNT growth on Mo substrates at temperatures 400 and 450 A degrees C, whereas at 350 A degrees C the structure as obtained, are CNFs. A significant change is observed on the as grown CNTs/CNFs morphology with the catalyst film pre-treatment time and the growth temperature. Prolonged catalyst pre-treatment at 400-450 A degrees C leads to growth of deformed structure CNTs which is due to the accumulation of amorphous carbon. At low temperature of 350 A degrees C, longer CNFs are obtained for longer treatment time. The growth mechanism can be explained based on the wettability of Ni film on Mo substrate and solubility of carbon atoms during growth process. Using field emission scanning electron microscopy and high resolution transmission electron microscopy, dimension and structure as well as crystallinity of the samples are analyzed. At synthesis temperatures of 450 and 400 A degrees C, multiwall carbon nanotubes are grown which shows some degree of crystallinity, whereas at 350 A degrees C CNFs are obtained which is confirmed by HRTEM analysis and Raman spectroscopy characterization.