Site-specific ion-irradiation is a promising tool fostering strain-engineering of freestanding nanostructures to realize 3D-configurations towards various functionalities. We first develop a novel approach of fabricating freestanding 3D silicon nanostructures by low dose ion-implantation followed by chemical-etching. The fabricated nanostructures can then be deformed bidirectionally by varying the local irradiation of kiloelectronvolt gallium ions. By further tuning the ion-dose and energy, various nanostructure configurations can be realized, thus extending its horizon to new functional 3D-nanostructures. It has been revealed that at higher-energies (∼30 kV), the nanostructures can exhibit two-stage bidirectional-bending in contrast to the bending towards the incident-ions at lower-energies (∼16), implying an effective transfer of kinetic-energy. Computational studies show that the spatial-distribution of implanted-ions, dislocated silicon atoms, has potentially contributed to the local development of stresses. Nanocharacterization confirms the formation of two distinguishable ion-irradiated and un-irradiated regions, while the smoothened morphology of the irradiated-surface suggested that the bending is also coupled with sputtering at higher ion-doses. The bending effects associated with local ion irradiation in contrast to global ion irradiation are presented, with the mechanism elucidated. Finally, weaving of nanostructures is demonstrated through strain-engineering for new nanoscale artefacts such as ultra-long fully-bent nanowires, nano-hooks, and nano-meshes. The aligned growth of bacterial-cells is observed on the fabricated nanowires, and a mesh based "bacterial-trap" for site-specific capture of bacterial cells is demonstrated emphasizing the versatile nature of the current approach.