Nanoparticles of iron carbides wrapped in multilayered graphitic sheets (carbon nanocapsules) were synthesized by electric plasma discharge in an ultrasonic cavitation field in liquid ethanol. The as-prepared material contained carbon nanocapsules but also included impurities such as amorphous carbon, graphite balls and flakes. These impurities must be removed to allow the development of applications for the carbon nanocapsules and, it is necessary to develop a suitable purification method to obtain samples of monodispersed carbon nanocapsules. Two purification methods were used. The first used a hydrogen peroxide solution and acid etching to remove the amorphous carbon and iron particles. These impurities were easily oxidized and dissolved in the solution and the graphite layers of the carbon nanocapsules were not damaged. The second used magnetic separation using permanent magnets to remove the graphite balls and flakes. Here, centrifugation was applied to separate the purified carbon nanocapsules around 100-200 nm in size.