The manipulation of magnetic anisotropy represents the fundamental prerequisite for the application of magnetic materials. Here we present the vectorial magnetic properties of nanostructured systems and thin films of Fe and FeCo prepared on linearly trenched Mo templates with thermally controlled periodicity. The magnetic properties of the nanosystems are engineered by tuning the shape, size, thickness, and composition parameters of the thin films. Thus, we control coercivity, magnetization, orientation of the easy axis of magnetization, and the long-range magnetic order of the system in the function of the temperature. We distinguish magnetic components that emerge from the complex morpho-structural features of the undulating Fe or FeCo nanostructured films on trenched Mo templates: (i) assembly of magnetic nanowires and (ii) assembly of magnetic islands/clusters. Uniaxial anisotropy at room temperature was proven, characterized, and explained in the case of all systems. Our work contributes to the understanding of magnetic properties necessary for possible further applications of linear systems and undulated thin films.