The imaging beam of a transmission electron microscope can be used to fine tune critical dimensions in silicon oxide nanostructures. This technique is particularly useful for the fabrication of nanopores with single-nanometer precision, down to 2 nm. We report a detailed study on the effect of electron-beam irradiation on apertures with various geometries. We show that, on the same wafer, pores that are smaller than a certain critical size shrink and that larger ones expand. Our results are in agreement with the hypothesis that surface-tension effects drive the modifications. Additionally, we have determined the chemical composition in the pore region before and after modifications and found no significant changes. This result proves that contamination growth is not the underlying mechanism of pore closure.