In this study, annealing of deep level (EL2) defect in gallium arsenide (GaAs) nanostructures by argon ion beam irradiation has been reported. GaAs nanodots of diameter ranging from 15 to 22 nm were deposited on silicon substratesusing the ions of GaAs generated by hot, dense and extremely non-equilibrium argon plasma in a modified dense plasma focus device. GaAs nanodots thus obtained were irradiated by Ar$^{2+}$ ion beam of energy 200 keV with varying ion fluences from $1 \times 10^{13}$ to $5 \times 10^{15}$ ions cm$^{−2}$ in the low energy ion-beam facility. The ion-beam irradiation transformed the as deposited GaAs nanodots into uniform GaAs nanostructured films of thickness $\sim$30 nm. The obtained nanostructured films are polycrystalline with paucity of arsenic antisite (EL2) deep level defect. The excess arsenic present in the as-deposited GaAs nanodots is the main cause of EL2 defect. Raman and photoluminescence measurements of GaAs nanostructured films indicates removal of excess arsenic, which was present in as-deposited GaAs nanodots, thereby suggesting annealing of EL2 defect from the ion-irradiated GaAs nanostructured films. The change in conductivity type from n- to p-type obtainedfrom Hall measurement further confirms annealing of EL2 defects. The ion-irradiated GaAs nanostructured films have low leakage current due to removal of defects as obtained in current–voltage study, which corroborate the annealing of EL2 defect. The defect-free GaAs nanostructured films thus obtained have potential applications in fabrication of highly efficient optoelectronic and electronic devices.