In this work magnetic nanowires Fe and Co were obtained by the electrodeposition method (DC and AC respectively) in anodic alumina template (AAO) with 200 nm pore diameter. The surfaces of both types of the magnetic nanowires were successfully chemically modified using 1-hexadecanethiol. Optional deposition method in the presence of external magnetic field obtained by permanent magnets in two orientations was conducted resulting in wires with different morphology. The quality of alumina pores was examined using SEM (Scanning Electron Microscopy). Free and clean nanostructures were studied by TEM (Transmission Electron Microscopy) techniques. In addition, the EDS (Energy Dispersive Spectroscopy) analysis was done to prove the composition of the obtained material. The results of functionalization were observed by IR (infra-red) spectroscopy. (C) 2011 Elsevier B.V. All rights reserved.