Silicon stencil masks for ion beam projection lithography have a protective layer stopping the ions and thus preventing a change in the Si membrane stress. This is needed to maintain extremely tight pattern placement specifications even when they are irradiated with high exposure doses. The fabrication of carbon protective layers by indirect sputter coating which are suitable for helium ion beam exposure has already been reported. This article describes a method of forming very low stress carbon protective layers based on direct radio frequency sputter coating with nitrogen added to the argon sputter gas and in situ thermal treatment using commercially available equipment. The carbon layers thus produced are stable in conventional environments. The article deals also with the physical characterization of carbon layers and the protection performances of these coatings under helium ion beam exposure using accelerated lifetime testing.