The disclosure relates to methods of beam pen lithography using a tip array having a plurality of transparent, elastomeric, reversibly-deformable tips coated with a blocking layer and apertures defined in the blocking layer to expose tip ends of the tips in the array. The tip array can be used to perform a photolithography process in which the tips are illuminated with a radiation that is channeled through the tips and out the apertures to expose a photosensitive substrate. Also disclosed are tip arrays formed of polymers and gels, apparatus including the tip arrays and radiation sources, and related apparatus for selectively masking tips in the tip array from radiation emitted from the radiation source.