Nanoscale materials are one of the few engineering materials that can be grown from the bottom up in a controlled manner. Here, the effects of nanostructure and nanoscale conformal coating on the mechanical behavior of vertically aligned carbon nanotube (CNT) arrays through experiments and simulation are systematically investigated. A modeling approach is developed and used to quantify the compressive strength and modulus of the CNT array under large deformation. The model accounts for the porous nanostructure, which contains multiple CNTs with random waviness, van der Waals interactions, fracture strain, contacts, and frictional forces. CNT array micropillars are grown and their porous nanostructure is controlled by the infiltration and deposition of thin conformal coatings using chemical vapor deposition. Flat-punch nanoindentation experiments reveal significant changes in material properties as a function of coating thickness. The simulations explain the experimental results and show the novel failure transition regime that changes from collective CNT buckling toward structural collapse due to fracture. The compressive strength and the elastic modulus increase exponentially as a function of the coating thickness and demonstrate a unique dependency on the CNT waviness. More interestingly, a design rule is identified that predicts the optimum coating thickness for porous materials.