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Carpet-like arrays of carbon nanotubes (CNTs) on graphitic carbon materials have been investigated in order to understand all-carbon hierarchical structures for multifunctional surface-active devices. Pure CNT carpets are seen to be super-hydrophobic as long as they are well aligned. For future applications involving aqueous environments, the ability to tailor the surface wettability and switch it on demand can be very useful, and enable unprecedented devices related to microfluidics, catalysis and sensing/detection systems. In this study, microwave plasma treatments were used to functionalize CNT carpets for a progressive increase in wettability so that they could eventually become super-hydrophilic. This change could be reversed by heating. Alternating between microwave plasma treatment and heating enabled repeated cycling of the CNT carpets between super-hydrophobic and super-hydrophilic states. This paper focuses on the influence of these two treatments on surface chemical states and multiscale morphology of CNT carpets, and their relation to wettability. It was shown by X-ray Photoelectron Spectroscopy (XPS) that oxygen-containing groups attached to surface carbon atoms are created during plasma treatment. These species desorb at temperatures of about 110 °C. The strength of C 1s and O 1s XPS signals from these radicals were seen to have direct correlation with water contact angles. In addition to surface chemistry, carpet morphology plays an important role in contact angle variations. Extreme surface roughness caused by high aspect-ratio of nanotubes would strongly accentuate both hydrophobic and hydrophilic behavior compared to flat surfaces. Classical geometric models of liquid droplets on uneven solids have been considered. Topological image analysis combined with intrinsic contact angle on flat graphene is used to predict the contact angle of these carpets, which matches well with experimental results. This analysis further explains why observed contact angles change if the vertical alignment of CNT is disturbed.