Complex structures often consist of many interconnected or "coupled" simpler regions. The problem frequently arises of determining the geometry of these individual subregions within the larger structure. We consider a simple model to argue that the high eigenmodes of the diffusion equation can be used to probe their geometry. We find that for a wide range of coupling, certain high eigenmodes preferentially remain within a particular subregion, thereby allowing the association of the corresponding eigenvalue with that subregion. We discuss an application of these results to the characterization of internal structure of porous media.