In this work, we use anodic aluminum oxide (AAO) templates to build NiFe magnetic nanohole arrays. We perform a thorough study of their magnetic, electrical and magneto-transport properties (including the resistance R(T), and magnetoresistance MR(T)), enabling us to infer the nanohole film morphology, and the evolution from granular to continuous film with increasing thickness. In fact, different physical behaviors were observed to occur in the thickness range of the study (2 nm < t < 100 nm). For t < 10 nm, an insulator-to-metallic crossover was visible in R(T), pointing to a granular film morphology, and thus being consistent with the presence of electron tunneling mechanisms in the magnetoresistance. Then, for 10 nm < t < 50 nm a metallic R(T) allied with a larger anisotropic magnetoresistance suggests the onset of morphological percolation of the granular film. Finally, for t > 50 nm, a metallic R(T) and only anisotropic magnetoresistance behavior were obtained, characteristic of a continuous thin film. Therefore, by combining simple low-cost bottom-up (templates) and top-down (sputtering deposition) techniques, we are able to obtain customized magnetic nanostructures with well-controlled physical properties, showing nanohole diameters smaller than 35 nm.