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Manipulation of electron beam irradiation using TEM determines the selective region with a particular size and depth to conduct the subsequent process for nanopore formation. • Recording the effect of e-beam irradiation on Mo 5 O 14 nanowires by in situ TEM. • Manipulating e-beam to define the anticipated region and the size of nanoporosity. • Atom removal and crystallinity degradation resulting in structural transformation. • The formation of nanopores due to the numerous broken bonds in crystalline Mo 5 O 14. • Revealing the mechanism of selective nanopore formation in nanoscale modification. The Mo 5 O 14 -type structure is representative of the MoO-based catalyst in the selective oxidation process. Single-crystalline Mo 5 O 14 nanowires can be synthesized in a controlled manner by chemical vapor deposition (CVD). A nanowire catalyst with a porous structure combines the advantages of both nanoparticles and nanowires, leading to a substantial increase in the specific surface area. Therefore, we aim to manipulate the e-beam irradiation process on Mo 5 O 14 nanowires to induce the nanoporous structures in selected regions. In situ transmission electron microscopy (TEM) enabled us to visualize the structural transformation through gradual e-beam irradiation. The e-beam irradiation process removes oxygen atoms and renders the internal structure unstable. After the irradiated region is exposed to air, atoms tend to escape to decrease the internal energy. This results in the formation of nanopores because of the irradiation effect. By nanoscale modification method, the irradiated region is controlled by the electron beam size, which determines the nanopore distribution in the selected region. The study is beneficial for increasing the surface area of Mo 5 O 14 -type catalysts with variable nanopore densities and for modifying nanomaterials using a convenient method. [ABSTRACT FROM AUTHOR]