Stacking-fault tetrahedra are detrimental defects in neutron- or proton-irradiated structural metals with face-centered cubic structures. Their removal is very challenging and typically requires annealing at very high temperatures, incorporation of interstitials or interaction with mobile dislocations. Here we present an alternative solution to remove stacking-fault tetrahedra discovered during room temperature, in situ Kr ion irradiation of epitaxial nanotwinned Ag with an average twin spacing of ~8 nm. A large number of stacking-fault tetrahedra were removed during their interactions with abundant coherent twin boundaries. Consequently the density of stacking-fault tetrahedra in irradiated nanotwinned Ag was much lower than that in its bulk counterpart. Two fundamental interaction mechanisms were identified, and compared with predictions by molecular dynamics simulations. In situ studies also revealed a new phenomenon: radiation-induced frequent migration of coherent and incoherent twin boundaries. Potential migration mechanisms are discussed.