Nanostructures may be exposed to irradiation during their manufacture, their engineering and whilst in-service. The consequences of such bombardment can be vastly different from those seen in the bulk. In this paper, we combine transmission electron microscopy with in situ ion irradiation with complementary computer modelling techniques to explore the physics governing the effects of 1.7 MeV Au ions on gold nanorods. Phenomena surrounding the sputtering and associated morphological changes caused by the ion irradiation have been explored. In both the experiments and the simulations, large variations in the sputter yields from individual nanorods were observed. These sputter yields have been shown to correlate with the strength of channelling directions close to the direction in which the ion beam was incident. Craters decorated by ejecta blankets were found to form due to cluster emission thus explaining the high sputter yields.