Materials with nanometer size heterogeneities are commonplace in the physical and biological sciences and often exhibit complex morphologies. Although this morphology has a dramatic effect on the materials' properties (e.g., transport and reaction processes), it is often difficult to accurately characterize. We describe a method, using a novel analysis of small angle x-ray scattering data, of generating representative three-dimensional morphologies of isotropic twophase materials (one class of heterogeneous materials) where the morphology is disordered. This is applied to thin films containing nanometer sized pores with a range of porosities (4-44%).These representations provide a visualization of the pore morphology, give the pore size scale and extent of interconnection, and permit the determination of the transitions from closed pore to interconnected pores to bicontinuous morphology. This methodology will be valuable for characterizing two-phase systems, such as polymer blends, microemulsions, porous geological materials, bones, cements and ceramics.