In order to ascertain the suitability of glassy carbon as a material for encapsulation of nuclear waste, glassy carbon was implanted with Xe and the structural changes and surface modification were investigated before and after annealing. This was performed using Raman spectroscopy analysis, high-resolution transmission electron microscopy (HRTEM) measurements, scanning electron microscopy (SEM), and atomic force microscopy (AFM). The Raman spectrum of the implanted sample showed that ion bombardment amorphised the glassy carbon structure. The HRTEM analysis of the virgin glassy carbon exhibited some features which are similar to those of fullerenes. One of the features is the appearance of closed onion-like nanoparticles and several graphitic fringes of varying sizes and orientations embedded in the glassy carbon structure. The presence of the onion-like features, as well as the graphitic fringes within the glassy carbon structure, suggest that glassy carbon is a disordered form of carbon. The HRTEM analysis of the as-implanted sample also shows some dark spots within the implanted region which are likely xenon bubbles. The SEM and AFM analysis showed that the grain size becomes larger and more prominent with increasing annealing temperature, leading to an increase in the surface roughness of glassy carbon.