This disclosure describes systems, apparatus, methods, and devices related to ion beams fabrication. A device may overlay a wafer assembly of one or more layers with a top layer comprised of a material having 2D material characteristics. The device may be fabricated by applying an ion beam targeted to at least one of one or more regions of the top layer or a resist layer placed on top of the top layer, wherein the ion beam is tuned using a predetermined energy range or a dosing level of ions to modify material characteristics of the resist layer or to perform milling of the top layer or other layers of the one or more layers of the wafer assembly.