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Magnetic configurations in heterostructures are often difficult to probe when the magnetic entities are buried inside. In this study we have captured magnetic and magnetoresistance “fingerprints” of Co nanodisks embedded in Co/Cu multilayered nanowires using a first-order reversal curve method. In 200 nm diameter nanowires, the magnetic configurations can be tuned by adjusting the Co nanodisk aspect ratio. Nanowires with the thinnest Co nanodisks exhibit single domain behavior, while those with thicker Co reverse via a vortex state. A superposition of giant and anisotropic magnetoresistance is observed, which corresponds to the different magnetic configurations of the Co nanodisks.