Probing surface order as well as the degree of structural modification in carbon nanotube systems is of fundamental importance for incorporation of these materials into practical functional devices. The current study pertains to the analysis of the surface order of vertically-aligned single-walled and multi-walled carbon nanotube arrays of varying length and composition by means of near-edge X-ray fine structure spectroscopy (NEXAFS). Both NEXAFS and scanning electron microscopy (SEM) studies concluded that the nanotubes in these samples were oriented vertically to the plane of the surface. However, NEXAFS polarization analysis provided a more quantitative and nuanced description of the surface structure, indicative of far less localized surface order, an observation partially attributed to misalignment and bending of the tubes. Moreover, it was demonstrated by NEXAFS that the surface order of the arrays was imperfect and relatively independent of the height of the nanotube arrays. In addition, we have shown that NEXAFS can be used to correlate the extent of chemical functionalization and oxygenation with disruption of the electronic and physical structure of nanotubes embedded in array motifs.