Exposed to ionizing radiation, nanomaterials often undergo unusual transformations compared to their bulk form. However, atomic-level mechanisms of such transformations are largely unknown. This work visualizes and quantifies nanopore shrinkage in nanoporous alumina subjected to low-energy ion beams in a helium ion microscope. Mass transport in porous alumina is thus simultaneously induced and imaged with nanoscale precision, thereby relating nanoscale interactions to mesoscopic deformations. The interplay between chemical bonds, disorders, and ionization-induced transformations is analyzed. It is found that irradiation-induced diffusion is responsible for mass transport and that the ionization affects mobility of diffusive entities. The extraordinary room temperature superplasticity of the normally brittle alumina is discovered. These findings enable the effective manipulation of chemical bonds and structural order by nanoscale ion-matter interactions to produce mesoscopic structures with nanometer precision, such as ultra-high density arrays of sub-10-nm pores with or without the accompanying controlled plastic deformations.