Embodiments of the present invention provide methods for fabricating graphene nanoelectronic devices with semiconductor compatible processes, which allow wafer scale fabrication of graphene nanoelectronic devices. Embodiments of the present invention also provide methods for passivating graphene nanoelectronic devices, which enable stacking of multiple graphene devices and the creation of high density graphene based circuits. Other embodiments provide methods for producing devices with graphene layer segments having multiple thicknesses.