A well-ordered nanopatterned structure has been obtained in sputtered magnetic thin films by self-assembling of polystyrene nanospheres. Arrays of holes in Co, Ni, and Ni80Fe20 films having a mean size ranging in the interval of 200–400 nm depending on the experimental condition have been prepared. Sample microstructure has been studied by scanning electron microscopy and atomic force microscopy. Room-temperature hysteresis loops have been measured in the parallel and perpendicular configuration (Hmax=20 kOe). Magnetoresistance (MR) measurements have been performed by means of a standard four-contact technique at several angles between the current and the magnetic field (Hmax=70 kOe) in the temperature interval of 4–200 K. An anisotropic MR effect has been observed in all compositions independent on the hole mean dimension. The role on magnetic and magnetotransport properties of either sample microstructure or composition has been studied in such patterned structures.