Magnetic scaffolds have been investigated as promising tools for the interstitial hyperthermia treatment of bone cancers, to control local recurrence by enhancing radio- and chemotherapy effectiveness. The potential of magnetic scaffolds motivates the development of production strategies enabling tunability of the resulting magnetic properties. Within this framework, deposition and drop-casting of magnetic nanoparticles on suitable scaffolds offer advantages such as ease of production and high loading, although these approaches are often associated with a non-uniform final spatial distribution of nanoparticles in the biomaterial. The implications and the influences of nanoparticle distribution on the final therapeutic application have not yet been investigated thoroughly. In this work, poly-caprolactone scaffolds are magnetized by loading them with synthetic magnetic nanoparticles through a drop-casting deposition and tuned to obtain different distributions of magnetic nanoparticles in the biomaterial. The physicochemical properties of the magnetic scaffolds are analyzed. The microstructure and the morphological alterations due to the reworked drop-casting process are evaluated and correlated to static magnetic measurements. THz tomography is used as an innovative investigation technique to derive the spatial distribution of nanoparticles. Finally, multiphysics simulations are used to investigate the influence on the loading patterns on the interstitial bone tumor hyperthermia treatment.