Deep proton writing (DPW) is a fabrication technology developed for the rapid prototyping of polymer microstructures. We use polymethylmethacrylate (PMMA) substrates, which act as a positive resist, for irradiation with a collimated 12-MeV energy proton beam. Using 12 MeV enables the irradiation of increasingly thick PMMA substrates with less conicity of the sidewalls compared to the lower energies used in previous work. A microhole of 47.7 μm diameter over a depth of 1 mm is achieved, leading to a maximum aspect ratio of 21∶1. The sidewalls of the irradiated structures show a slightly conical shape and their root-mean-square surface roughness is lower than 50 nm averaged over 72 measured areas of 56 μm×44 μm. This means that DPW components have optical surface quality sidewalls for wavelengths larger than 400 nm. Based on the trade-off among the sidewall roughness, conicity, and the development time, we determine that the optimal proton fluence for 12-MeV DPW in PMMA is 7.75×106 μm−2. Finally, we discuss some high aspect ratio microstructures with optical surface quality that were created with DPW to be used for a myriad of applications, such as micromirrors, microlenses, optofluidic devices, and high-precision alignment structures for single-mode optical fiber connectors.