Carbon Nanotubes (CNTs) exhibit exceptional properties in terms of high strength-to-weight, high electrical conductivity, and high thermal conductivity, and have been employed as a reinforcement in various composites and other materials. Their tolerance to radiation environments may be suggested by their response to energetic ion bombardment. We discuss the effects of argon ion bombardment of both thin and thick multiwall carbon nanotube films over a range of 4 to 11 keV at fluence levels up to the order of 1021 ions/cm2. While individual carbon atoms are readily displaced from a carbon nanotube by bombardment at these energies, these nanotubes also exhibit a self-healing capability. At moderate energies and fluence, if two or more carbon nanotubes are touching and an ion strikes this point, they heal together where a junction or cross-link between them is created and the nanotubes interpenetrate. Even though some of the properties of the carbon nanotubes may be degraded by ion bombardment at non-junction regions, we have demonstrated a bulk cross-linked thin film of randomly oriented multiwall carbon nanotubes with an isotropic thermal conductivity of 2150 W/m K. At higher energies and fluence, the carbon nanotubes appear to collapse and reform aligned parallel to the incoming ion bombardment trajectory, producing high aspect ratio tapered structures. These structures are, in general, fully dense, unlike the loosely packed random carbon nanotube array from which they originated. There is also a sharp transition at the base of these structures from the dense form to the loose-packed form, suggesting that these structures may inhibit further penetration of the energetic ions.