In this article, the limits of thin-film deposition on very rough topographies are demonstrated by depositing alumina on vertically aligned carbon nanotubes (VACNTs). Vapor deposition techniques are the enabling platforms of the thin-film industry, offering high material versatility and good coverage ability on relatively flat surfaces, leading to frequent use in a large array of applications, especially nanoscale electronic devices such as sensors and electrodes. However, when surface topography exhibits high roughness, even depositions that are not limited to line-of-sight show only partial coverage, significantly hindering performances. Our manufacturing process of VACNT/Al2O3 nanocomposites has three vaporous steps: CNT growth by chemical vapor deposition (CVD), functionalization via controlled thermal oxidation, and atomic layer deposition (ALD) of alumina. The same limited accessibility hinders each of these three steps. Morphological analyses show different CNT heights throughout the sample, with shorter CNTs in the middle, having less access to gases. As height differences between the center and peripheries escalate, sample centers may collapse under the tension. The limited accessibility of the center is manifested also in inhomogeneous oxygen contents, between sample centers and peripheries. Finally, a sharp transition in deposition quality occurs during the deposition process of Al2O3, from homogeneous to inconsistent, which is also linked to the accessibility differences between. Adjusting process parameters, we have successfully coated 1.8 mm-tall VACNT arrays with a homogeneous thin (few nm) Al2O3 layer and were able to increase the depth at which, thick (few dozens of nm) Al2O3 coating is uniform from 20 to 350 μm. However, when VACNTs were functionalized, the penetration depth was found to correlate negatively with center oxygen content. These results, indicating diffusion as a rate-setting step in complex topography coatings, can significantly improve deposition quality and enhance the performance of thin-film applications such as membranes, sensors, and electrodes for energy harvesting and storage.