Three-dimensional (3D) architectures obtained by the structural assembly of 1D nanomaterials are regarded as the next generation building blocks for sensors, electronics, photonics, and bioelectronic applications. Purification and functionalization of such 3D ordered structures are crucial for realizing their full potential. Plasma functionalization, compared to any solution based process, is favorable in retaining the alignment while functionalizing such structures. However, the commonly employed plasma processes like O2 or Ar plasma can be highly detrimental to well-aligned ordered nanostructures and thus might affect the properties intimately associated with their 3D structure. Here, for the first time, we investigate the mild nature of a radio frequency CO2 gas plasma as an effective source for purification and functionalization of vertically aligned CNT structures and study the effects of this functionalization onto the purification and functionalization by physical and chemical techniques (HRTEM, XPS, Raman). We found that CO2 plasma selectively etches the amorphous carbon present in the vertically aligned CNT structure. Moreover, it is as effective as the widely used but more aggressive O2 plasma in functionalizing the CNT. Unlike an O2 or Ar plasma, CO2 plasma has the tremendous advantage of retaining the structural integrity of the CNT structures. © 2014 American Chemical Society.