ours does not approximate the physical layout or limit the number of constituent materials, providing a more accurate and flexible design tool. We calculate critical currents, current phase relationships, and the energy gap where relevant. We validate our model by comparing it with published data. Through our analysis, we found that using multilayer films significantly enhances control over these quantities. For nanobridge junctions in particular, multilayer structures improve qubit anharmonicity compared to monolayer junctions, offering a substantial advantage for qubit performance. For coated multilayer microwave circuits it allows for better studies of the proximity effect, including their effective kinetic inductance.