Highly ordered alumina pore channel arrays are used as templates for the fabrication of magnetic nanowire arrays. These well-defined templates are based on the approach by Masuda and Fukuda and have an interpore distance of 65 and 100 nm and a monodisperse pore diameter of ≍30 nm. The pore channels are hexagonally arranged in 2D-domains, which extend over more than ten interpore distances. Nearly 100% metal filling of the alumina pore structures is obtained by a novel pulsed electrodeposition technique. Due to the high ordering degree of the nanowires arrays, we detect a squareness of ≍100% and coercive fields of 1200 Oe in the direction of the nanowires. The MFM measurements have been carried out by applying magnetic fields on magnetized and demagnetized samples to study the switching behavior of individual nanowires inside the arrays. Magnetic wires have been locally switched by a strong MFM tip and a variable external magnetic field. The MFM results show a good agreement with the bulk magnetic hysteresis loops.