The AC dielectrophoresis-induced separation of metallic and semiconducting single-wall carbon nanotubes has been carried out in a continuous flow microfluidic system with isolated electrodes. The separation has been studied for single-wall carbon nanotube aqueous suspensions with ionic (sodium dodecylsulphate) and non-ionic (TritonX-100) surfactants. The efficiency of separation has been determined with the help of resonant Raman spectroscopy using various excitation energies. The prototype microfluidic cell presently shows somewhat inferior separation efficiency with respect to static dielectrophoretic filtering on arrays of microelectrodes but has potential for improvements. Factors influencing the separation efficiency and scaling up of the process are discussed.