Recent advances in helium ion microscopy (HIM) have enabled the use of fine-focused He+ beams to image and shape materials at the nanoscale. In addition to traditional ion milling, the beam can also be used to induce reactions, such as cross-linking, in films of organic molecules. Here, we compare the use of focused ion and electron beams to fabricate spatially-defined cross-linked features in nanometre-thick films of tetracene. Ion and electron beam treatments were performed using the focussed energetic beams in a HIM and a scanning electron microscope, respectively. The patterned samples were analysed by optical microscopy, HIM, atomic force microscopy and nanoindentation. For samples fabricated using both energetic beams, the total deposited particle dose could be used to modify the optical properties, thickness and hardness of the dosed regions. X-ray photoelectron spectroscopy revealed that the dosed regions exhibited a higher sp3 content, consistent with crosslinking; rinsing in solvent showed that the patterned regions were insoluble and could be isolated by removing the unmodified film through dissolution. These molecular nanopatterns demonstrate the promise for ultrahigh resolution chemical lithography, and for fabrication of nanocomponents with tailored physical properties.