Carbon nanotubes filled with iron nanowires (Fe@CNTs) show magnetic anisotropy because of the high aspect ratio of the nanowires and are expected to find numerous applications such as magnetic recording media, probes for scanning force microscopy and medical treatment for cancer (hyperthermia). These applications require precise control of Fe@CNT growth. This growth depends on the condition of the substrate surface on which the CNTs are grown. In this study, Fe@CNTs were synthesized by thermal chemical vapor deposition on various thin metal films (Fe, Ni, Co, Al, Pt, Ti, or Mo) deposited on SiO2/Si(100) substrates using ferrocene as a precursor, and their growth characteristics were investigated. The growth clearly depends on the metal species incorporated in the thin films. Magnetic properties correlated with growth morphologies. Therefore, the appropriate selection of an underlayer is important for controlling magnetic characteristics of Fe@CNTs.