Accompanying the need for green energy generation is a need for energy storage systems since most green energy sources like solar and wind are intermittent. In recent times, much research focus has been placed on providing more durable and higher capacity energy storage devices like supercapacitors, which has led to the design of better electrode materials for these supercapacitors. Graphitic carbon nanotubes have been tipped as superior materials for making supercapacitors because of their unique electrical properties and pore structure. They are inert, lightweight, have high electrical conductivity, high thermal stability and very high surface areas especially when aligned. As a result, they are very suitable as electrode templates because thin nanosheets or nanoparticles can be embedded within them in a high surface area configuration without excessively sacrificing ion accessibility and electrical conductivity. We report the use of aligned carbon nanotubes as supercapacitor electrode templates and highlight their superiority, as a result of a better ordered pore structure, to entangled or collapsed carbon nanotubes for electrode applications. Specifically, we use Ni-Co mixed oxide and Co-Mn mixed oxide spinels characterized using EDX and XRD as electroactive materials. These spinels have been chosen because of their relatively high electrical conductivity and are optimized for relative metal ratios. Different methods of electrochemical deposition were also explored to achieve uniform coating. However, one challenge associated with using aligned carbon nanotube templates is the resistance between the current collector and the nanotubes. It is well known that an insulating alumina layer is necessary for the sustained and efficient growth of self-aligned nanotubes. In trying to overcome this challenge, we added a molybdenum layer to reduce the resistive effect of the alumina layer. Another challenge is the capillarity induced collapse of the nanotube forest between electrodeposition and annealing during the preparation of the electrode. Our approach to solving this involved the use of a new universally applicable method: specifically supercritical drying to preserve pore structure and prevent forest collapse during annealing after electrodeposition on self-aligned carbon nanotube forests. We highlight the effects each of these processes on the eventual capacitive performance of the prepared electrodes.