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Focused Ion Beam (FIB) is one of the most common methods for nanodevice fabrication. However, its implications on mechanical properties of polymers have only been speculated. In the current study, we demonstrated flexural bending of FIB-milled epoxy nanobeam, examined in situ under a transmission electron microscope (TEM). Controllable displacement was applied, while real-time TEM videos were gathered to produce morphological data. EDS and EELS were used to characterize the compositions of the resultant structure, and a computational model was used, together with the quantitative results of the in situ bending, to mechanically characterize the effect of Ga+ ions irradiation. The damaged layer was measured at 30 nm, with high content of gallium (40%). Examination of the fracture revealed crack propagation within the elastic region and rapid crack growth up to fracture, attesting to enhanced brittleness. Importantly, the nanoscale epoxy exhibited a robust increase in flexural strength, associated with chemical tempering and ion-induced peening effects, stiffening the outer surface. Young’s modulus of the stiffened layer was calculated via the finite element analysis (FEA) simulation, according to the measurement of 30 nm thickness in the STEM and resulted in a modulus range of 30–100 GPa. The current findings, now established in direct measurements, pave the way to improved applications of polymers in nanoscale devices to include soft materials, such as polymer-based composites and biological samples.