Earlier research has sought to utilize the exceptional thermal conductivity of CNTs to produce a heat spreader by bulk cross-linking the CNTs into an interpenetrating network. An isotropic thermal conductivity of 2150 W/m-K was measured in a 5 μm thick MWCNT film which had been subject to argon ion bombardment with an ion energy of 4 keV and a fluence on the order of 1017 ions/cm2 . While energetic ions will randomly bombard the entire CNT network, on occasion, one will strike a junction where two or more CNTs are touching, momentarily disrupting them. CNTs have the remarkable ability to self-heal, and in doing so, the disrupted junction self-heals into a new interpenetrating junction. However, practical heat spreader applications require films at least 100 times thicker than this initial demonstration. To achieve this, substantially higher ion energies and fluence were applied. But rather than forming interpenetrating junctions deeper into the bulk of a CNT thick film, an interesting new form of high aspect ratio structure results, where groups of CNTs are now vertically aligned, even though the original CNT thick film was randomly oriented. There is also a sharp transition at the base of these structures from the new aligned form to the original randomly oriented form. We consider various aspects of ion-induced sputter dynamics coupled to the growth processes of CNTs to account for these new aligned high aspect ratio structures. The role of ion channeling within and between CNTs is also considered.