Carbon nanotubes-transition metal oxide systems are intensively studied due to their excellent properties for electrochemical applications. In this work, an innovative procedure is developed for the synthesis of vertically aligned multi-walled carbon nanotubes (VACNTs) coated with transition metal oxide nanostructures. VACNTs are grown by plasma enhanced chemical vapor deposition and coated with a manganese-based metal organic precursor (MOP) film based on manganese acetate solution. Subsequent UV pulsed laser irradiation induces the effective heating-decomposition of the MOP leading to the crystallization of manganese oxide nanostructures on the VACNT surface. The study of the morphology, structure and composition of the synthesized materials shows the formation of randomly oriented MnO2 crystals, with few nanometers in size, and to their alignment in hundreds of nm long filament-like structures, parallel to the CNT's long axis. Electrochemical measurements reveal a significant increase of the specific capacitance of the MnO2-VACNT system (100 F g-1) as compared to the initial VACNT one (21 F g-1).