The objective of this work was a development of the Carbon nanoparticles doped with ferromagnetic iron oxide and clusters of cobalt atoms synthesized via a novel technology which combines the method of pyrolysis of ethanol vapors and the chemical vapor deposition (CVD) process in horizontal continuous reactor with certain temperature gradients and controlled partial oxygen pressure. Scanning Electron Microscope (SEM) and Auger Electron Spectroscopy (AES) studies of synthesized magnetic carbon nanopowders showed that under freely deposited state in the absence of the external magnetic field, the nanopowder consists of the randomly distributed carbon nanoparticles’ aggregates of 200 nm diameter doped with the magnetic clusters. Under the exposure to the low external magnetic field (~0.01 T) the nanoparticles were assembled into the large scale linear nano-chain structures.