Nanopatterned arrays of discrete cobalt nanostructures showing characteristic parameter-dependent sizes are formed from continuous thin films on a carbon nanotube substrate using millisecond pulsed intense UV light. The nanoparticles exhibit ferromagnetic behavior with magnetic remanence and coercivity depending on the particle size. The end-state particle size is shown to be a function of initial thin film thickness and excitation energy and is therefore tunable. The evolutionary process from continuous thin films to a discrete morphology is thermodynamically driven by the large surface energy difference between metastable thin films and the underlying carbon nanotube substrate. Evidence of the Danielson model of the dewetting process is observed. These arrays can find applications as platforms for the self-assembly of magnetically susceptible materials, such as iron or nickel nanostructures, into a conduction matrix for applications in energy extraction from a latent heat storage device.