Embodiments described herein provide for post deposition anneal of a substrate, having an amorphous carbon layer deposited thereon, to desirably reduce variations in local stresses thereacross. In one embodiment, a method of processing a substrate includes positioning a substrate, having an amorphous carbon layer deposited thereon, in a first processing volume, flowing an anneal gas into the first processing volume, heating the substrate to an anneal temperature of not more than about 450° C., and maintaining the substrate at the anneal temperature for about 30 seconds or more. Herein, the amorphous carbon layer was deposited on the substrate using a method which included positioning the substrate on a substrate support disposed in a second processing volume, flowing a processing gas into the second processing volume, applying pulsed DC power to a carbon target disposed in the second processing volume, forming a plasma of the processing gas, and depositing the amorphous carbon layer on the substrate.