Physical properties of magnetic nanostructures and devices strongly depend on the morphological characteristics of their various components. This is especially true and becomes particularly complex in hybrid nanostructures, where soft organic molecules are at the vicinity of ferromagnetic metallic films. The supramolecular architecture of molecular films embedded between iron (Fe) and cobalt (Co) layers, has been investigated by ferromagnetic nuclear resonance (FNR). In such sample architecture, the presence of pin holes in the organic layers is detected by FNR contributions in a specific spectral range. The methodology that has been developed allows probing the continuity and packing of zinc tetra-phenyl porphyrin (ZnTPP) molecular films between the Co and Fe films. The experimental results suggest that, regardless of the nature of the ferromagnetic under-layer, at least 15 monolayers of ZnTPP are necessary to form continuous and pin-hole free molecular films. In addition, quantitative analyses show that ZnTPP layers exhibit distinct morphologies that are dependent on the nature of the ferromagnetic metallic under-layer.