Could you please elaborate more? From what I understood, you have metal bodies and non-metal bodies in each layer. These are all 3D bodies. Correct me if I am wrong here.
You can use Steady State Thermal analysis system in Workbench. In the Geometry cell, you can import tis Spaceclaim model. In Thermal analysis, you can use contact between bodies or in Spaceclaim you can create ‘Share topology’ so when meshed, they create shared nodes between separate bodies. You might also need to use Boolean operation in Spaceclaim to remove overlapping volumes if any.You may check these courses.