When you export moi stuff, you can select which items to export. You can do it by styles or by object name, for instance. You can save those as separate mesh layers, then import them separately into one scene in say, Modo or C4D. You can create your layers there as you go along. I agree with Michael - Rhino is the last application I would use to handle polygon meshes. It's not designed for it, and no other app uses .3dm as an import format for poly meshes.