This proposal introduces a novel dark field X-ray Reflectivity (DFXRR) technique to overcome the limitations of traditional characterization methods for small layered junctions used in quantum applications. These junctions, comprising thin films of conductors or superconductors separated by oxide layers, are crucial in devices like Josephson junctions and SQUIDs but challenging to analyze due to their small size and complex composition. Traditional methods like SEM and TEM are often limited and destructive, while standard XRR lacks the necessary in-plane resolution. DFXRR offers a breakthrough by enabling spatial mapping at each incidence angle, allowing for the non-destructive reconstruction of detailed 3D electron density maps. This method aims to provide unparalleled insights into layer thickness, density, and roughness, significantly advancing our understanding of quantum device structures and phenomena.