Polymer membranes are conventionally prepared using high-energy particles from radioactive decay or by the bombardment of hundreds of MeVs energy ions. In both circumstances, tracks of damage are produced by particles/ions passing through the polymer, and successively, the damaged material is removed by chemical etching to create narrow pores. This process ensures nanosized pore diameter but with random placement, leading to non-uniform local pore density and low membrane porosity, which is necessary to reduce the risk of their overlapping. The present study is focused on the use of polyethylene terephthalate (PET) foils irradiated by 10.0 MeV carbon ions, easily achievable with ordinary ion accelerators. The ion irradiation conditions and the chemical etching conditions were monitored to obtain customized pore locations without pore overlapping in PET. The quality, shape, and size of the pores generated in the micromembranes can have a large impact on their applicability. In this view, the Scanning Transmission Ion Microscopy coupled with a computer code created in our laboratory was implemented to acquire new visual and quantitative insights on fabricated membranes.