The ability to form patterned surface nanostructures has revolutionized the miniaturization of electronics and led to the discovery of emergent behaviors unseen in macroscopic systems. However, the creation of such nanostructures typically requires multiple processing steps, a high level of technical expertise, and highly sophisticated equipment. In this work, we have discovered a simple method to create nanostructures with control size and positioning in a single processing step using a standard scanning electron microscope. The technique can be applied to a wide range of systems and was successful in every layered material tested. Patterned nanostructures were formed on graphite, topological insulators, novel superconductors, and layered transition metal dichalcogenides. The nanostructures were formed via the incorporation of carbon nanoparticles into the samples in a novel form of intercalation. It appears that the electron beam interacts with residual organic molecules available on the sample surface, making it possible for them to intercalate between the layers in their crystal structure and break down into carbon. These carbon nanoparticles have strong broad-wavelength interactions in the visible light range, making these nanostructures easily detectable in an optical microscope and of interest for a range of nanoscale electro-optical devices.