Precise patterning of polymer-based biomaterials for functional bionanostructures has extensive applications in biomimetics, biosensing, tissue engineering, and regenerative medicine. Here, we provide a critical review of recent progress in the nano-manufacture of biopolymers, including those for both natural and genetic purposes, with an emphasis on processing using electron and ion beams. In this review, we aim to provide in-depth coverage of nanomanufacturing processing technologies as well as the application of these new technologies. This will demonstrate how structural biopolymers, with silk proteins in particular as an example, can be considered as a material platform with a revolutionary impact in the biomedical, photonic and electronic fields.