3D simulations and meshing problems

Hello,

I am doing some 3D simulations. I have basically some very small structures on a bigger substrate. I have to use the ignore faces operation to remove the common faces between the substrate and those small structures. And This make the whole geometry as just one domain so I won’t be able to refine the mesh just on those small stretchers, is there any way to solve this problem please?

I do appreciate any suggestions