Because of their extremely large surface art a, carbon nano tubes (CNTs) and carbon nano fibers (CNFs) have been widely used to remove heavy metals from water. But the removal of such CNTs and CNFs from water is another important aspect in water purification process. In the present work, we discuss CNT and CNF separation from water using a magnetic separation technique. In order to compare the separation efficiencies, CNTs and CNFs having wide variation in their magnetic properties were selected. The effects of CNT and CNF concentrations in untreated water and water now velocity on the separation efficiency were investigated systematically.