Carbon nanotubes were synthesised with a high density on a large area of a platinum pre-patterned layer of silicon nitride by the chemical vapour deposition of acetylene at 500 °C in ammonia. The effect of microwave induced thermal annealing on the morphology and electrical transport properties of the nanotube films has been evaluated. At increasing annealing times the thermal treatment leads to a progressive reduction of the nanotube mean diameter, and to a considerable rise in resistance of the nanotube films. Such modifications are attributed to a strong reduction of the amorphous carbon content as a consequence of the thermal annealing.