In this work, we attempt to purify multi-walled carbon nanotubes (MWNTs) using electrophoresis induced by application of an ac electric field to a set of microelectrodes in a microliquid channel. This purifying method is different from conventional methods based on chemical processes. We observed that the most of the MWNTs could pass along the microliquid channel without attaching to the electrode under specific conditions of 1 kHz, 0.2 Vrms/μm. On the other hand, the majority of the carbon impurities attached to the electrodes under same condition. Field emission scanning electron microscopy (FESEM) images confirm that this condition is beneficial for removing the carbon impurities. We aligned and attached this purified MWNTs and raw materials to extra electrodes with 5 MHz, 0.8 Vrms/μm. This experimental FESEM images show a clear difference between before and after purification. The proposed approach has potential applicability to the development of microdevices that can simultaneously perform purification and fabrication of MWNTs.