Multiwalled carbon nanotubes were purified and size-separated by a multistep microfiltration process through a sequence of track-etched polycarbonate membranes of various pore sizes in both dead-ended and cross-flow mode. For this cascade microfiltration, the electric arc derived raw multiwalled samples were suspended in an aqueous solution of sodium dodecyl sulfate in deionized water. By examining the deposits on the membrane surfaces and in the permeate suspensions with scanning electron microscopy and atomic force microscopy, the nanotube fractionation was confirmed and analyzed. These scanning techniques showed that the components of the crude sample, which included carbon nanotubes, polyhedral nanoparticles, and large aggregates, were separated from each other during the filtration. In addition, fractionation of the multiwalled carbon nanotubes according to length was possible.