Ordered arrays of magnetic carbon nanotubes have been obtained by means of non-catalytic chemical vapor deposition, by growing nanotubes inside porous alumina templates and subsequently filling them with Fe3O4 particles. Magnetic properties of the arrays have been studied at different temperatures using vibrating sample magnetometry and ferromagnetic resonance. The filled nanotubes have exhibited superparamagnetic properties with a blocking temperature of about 145 K. The average nanotube filling factor, as determined by the magnetometry, was 32%, while the ferromagnetic resonance has detected the presence of conglomerates of nanoparticles. This allowed us to conclude that the filling of the nanotubes with the magnetic phase was non-uniform. Such magnetic carbon nanotubes have the potential of being used in a wide range of applications, in particular, in the production of nanofluids, which can be controlled and steered by appropriate magnetic fields. The proposed methodology opens an opportunity for simplified fabrication of magnetic nanotubes aiming at biomedical applications and, in particular, at the production of magnetic nanofluids which can be steered by appropriate magnetic fields, e.g., as magnetic sorbents for cleaning blood from free hemoglobin. The first experimental results have shown that our proposed magnetic nanoseparation is of more than tenfold efficiency in comparison with the conventional hemosorption method.