Minimal proximity effect coupled with uniform energy deposition in thin polymer layers make Proton Beam Writing (PBW) an intuitive direct-write lithographic technique. Feature sizes matching the focused beam spot size have been fabricated in photoresists down to 19nm. Reproducible sub-10nm beam focusing will make PBW a promising contender for sub-10nm lithography. In this paper, we present beam size characterization by imaging a PBW resolution standard using transmitted/scattered ions and secondary electrons. Using Scanning Transmission Ion Microscopy (STIM) spectra for 1 and 2MeV H2+ beams, we experimentally measure the thickness of the resolution standard to be 0.9±0.1μm, applying two independent calibration methods, which match the original intended thickness during fabrication. Through bias optimization of a Micro-Channel Plate (MCP), we show a tuneable secondary electron detection per proton for imaging with a maximum of 75% e/p for a beam of 1MeV H2+. Based on STIM mode beam size measurement, we discuss considerations for quadrupole system alignment in order to remove higher order translational and rotational misalignments critical to achieve sub-40nm spot sizes. A spot size of 13×32nm2 (STIM) was achieved using a newly developed interface, capable of autofocusing ion beams and performing PBW.