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The discovery of carbon nanotubes has opened the door to numerous cutting-edge nanoscale research fields including microelectronic devices, and biomedical application. Although pure nanotubes suffice for most purposes, highly pure magnetic carbon nanotubes are more suitable for specialized applications such as gene delivery. The conventional purification methods of carbon nanotubes are too harsh for the nanotubes to retain any magnetic characteristics, hence to enable the nanotubes be sensitive to magnetic field. It requiresthe reloading of metallic particles inside or on the surface of each tube. Instead, this paper proposes an innovative purification method to extract magnetic carbon nanotubes from arc-discharged single-walled carbon nanotube material. The procedure is easy to execute and time-saving. TEM and AFM images are used to monitor the purification process and prove that the carbon nanotube retain magnetic characteristics after the purification process.