I know that mamoset recognizes objects with multiple material IDs, but when it comes to baking them, everything gets sandwiched into one map.
Obviously I could break up the pieces of the mesh and re-import, but is there a workflow to do it without needing to separate the object? Just curious.
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The typical workaround would be to have multiple baker objects in your scene, and make sure that the lowpoly objects for each do not have overlapping uvs. So generally you would want to offset or not include any uvs that don't apply to the material ID you're baking for that object.