Arc-synthesized single-walled carbon nanotubes have been purified through preparative electrophoresis in agarose gel and glass bead matrixes. Two major impurities were isolated: fluorescent carbon and short tubular carbon. Analysis of these two classes of impurities was done. The methods described may be readily extended to the separation of other water-soluble nanoparticles. The separated fluorescent carbon and short tubule carbon species promise to be interesting nanomaterials in their own right.