Deep proton writing (DPW) is a fabrication technology developed for the rapid prototyping of polymer micro-structures. We use SU-8, a negative resist, spincoated in a layer up to 720 lm-thick in a single step on borosilicate glass, for irradiation with a collimated 12 MeV energy proton beam. Micro-pillars with a slightly conical profile are irradiated in the SU-8 layer. We determine the optimal proton fluence to be 1.02 Â 10 4 lm À2 , with which we are able to repeatably achieve micro-pillars with a top-diameter of 138 ± 1 lm and a bottom-diameter of 151 ± 3 lm. The smallest fabricated pillars have a top-diameter of 57 ± 5 lm. We achieved a root-mean-square sidewall surface roughness between 19 nm and 35 nm for the fabricated micro-pillars, measured over an area of 5 Â 63.7 lm. We briefly discuss initial testing of two potential applications of the fabricated micro-pillars. Using $100 lm-diameter pillars as waveguides for gigascale integration optical interconnect applications, has shown a 4.7 dB improvement in optical multimode fiber-to-fiber coupling as compared to the case where an air-gap is present between the fibers at the telecom wavelength of 1550 nm. The $140 lm-diameter pillars were used for mold fabrication with silicone casting. The resulting mold can be used for hydrogel casting, to obtain hydrogel replicas mimicking human tissue for in vitro bio-chemical applications.