ABSTRACTIn this work, we explored the capabilities of energetic focused beams of light ions for the fabrication and analysis of microstructures produced on commercial polyethylene terephthalate (PET) foils. To that end, single lines and multi‐structure patterns were drawn directly on the foils using Proton Beam Writing (PBW) techniques followed by chemical etching. The characterization of the microstructures was carried out with on‐axis Scanning Transmission Ion Microscopy (STIM) employing H+1, He+2, and Li+3 ions in the MeV range. Scanning Electron Microscopy (SEM) was employed as well. The results show that a polymer like PET can be patterned trough a proper combination of irradiation parameters and etching times. However, aspect ratios obtained in this way are quite poor. Moreover, STIM images obtained from different regions of the ion energy spectra reveal patterns and cavities seen neither by conventional STIM, where the whole energy spectrum is used, nor by SEM. Moreover, striking differences are observed when different ions are used for STIM analysis. The results suggest that heavier ions provide additional information of the structures under analysis when compared with usual STIM employing protons. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016, 133, 43253.