High resolution transmission electron microscopy (HREM) reveals that MeV heavy ions like Au generate radiation damage defects, a few nanometers in size, in surface regions (about 100 Å) of the superconductors. Much larger defects have been found in the deeper regions of the superconductor sample, which is believed to be due to the larger damage cascade created by the slower ions after their electronic energy loss along the track. Monte Carlo simulation (trim) shows the same result in damage size as the HREM study. Light ions, like protons, generate mostly point defects, which are not visible to current electron microscopy. These point defects, although they can pin the flux, are not ideal for flux pinning, due to their small sizes.