Fe-based multiwalled carbon nanotubes (MWCNT) have been studied for more than a decade, owing to their numerous potential applications (hyperthermia cancer therapy, magnetic data storage etc.). However, to our knowledge, no neutron total scattering measurements have been carried out, and the local magnetic and atomic structure remain unknown. Our approach is to perform measurements at various temperatures on two different samples of Fe-based MWCNT (radial and flower-like structures), continuously filled by Fe. The radial structures nanowires are filled by alpha-Fe, gamma-Fe and Fe3C, while the nanowires encapsulated by the flower-type structures are entirely filled by alpha-Fe. The objective is to understand the local atomic structure of this material and to study its magnetic structure to bridge the gap between synthesis and applications