This study investigated carbon nanotube filtration technology using catalyst particles supported on silicalite-1–biomorphic carbon materials (BCMs). Aqueous solutions of Mn(II), Cu(II), Cr(III), Cd(II), and Pb(II) were used to test the efficiency of heavy metal ions removal. Carbon nanotubes (CNTs) were synthesized and grown on BCMs by the chemical vapor deposition method catalyzed with the catalyst (Co, Fe, and Ni). The synthesized CNTs with Co– and Fe– nanoparticles were typically multi-walled carbon nanotubes, and they showed good crystallinity (ID/IG = 1.05) and yield of (11.10 and 8.86) %. The removal efficiency of Mn(II), Cu(II), Cr(III), Cd(II), and Pb(II) ions using Co-catalyzed CNT filter was 97.57%, 98.01%, 97.89%, 97.42%, and 99.99%, respectively.