Lithography techniques are currently being developed to fabricate nanoscale components for integrated circuits, medical diagnostics and optoelectronics. In conventional far-field optical lithography, lateral feature resolution is diffraction-limited. Approaches that overcome the diffraction limit have been developed, but these are difficult to implement or they preclude arbitrary pattern formation. Techniques based on near-field scanning optical microscopy can overcome the diffraction limit, but they suffer from inherently low throughput and restricted scan areas. Highly parallel two-dimensional, silicon-based, near-field scanning optical microscopy aperture arrays have been fabricated, but aligning a non-deformable aperture array to a large-area substrate with near-field proximity remains challenging. However, recent advances in lithographies based on scanning probe microscopy have made use of transparent two-dimensional arrays of pyramid-shaped elastomeric tips (or 'pens') for large-area, high-throughput patterning of ink molecules. Here, we report a massively parallel scanning probe microscopy-based approach that can generate arbitrary patterns by passing 400-nm light through nanoscopic apertures at each tip in the array. The technique, termed beam pen lithography, can toggle between near- and far-field distances, allowing both sub-diffraction limit (100 nm) and larger features to be generated.