This paper reports a multi-walled carbon nanotube (MWNT) cluster-based process for removing bacteria by uniquely combining the two excellent properties of carbon nanotubes (CNTs): magnetic susceptibility and bacterial affinity. The reaction system consisted of large clusters of MWNTs for bacterial capture and an external magnet for bio-separation. The designed system was tested using four different bacteria strains, including both gram-positive and gram-negative bacteria. The results demonstrated CNTs' excellent potential as highly effective bacterial adsorbents for the spontaneous adsorption of any types of bacteria to the clusters and as highly effective paramagnetic complexes for the rapid and highly effective magnetic separations. The CNT based system would be beneficial to many biomedical as well as environmental applications that require bacterial removal, including antimicrobial treatment, graft and implant purification, water purification, food processing, and biosensing of pathogens.