If you are trying to create masks for a complex Blender mesh in Substance, This is how youi would do it:
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Set up your vertex coloring areas in Blender, build your UV map, and export to FBX.
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Import the mesh into Substance, and then bake the mesh.
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Select only the ID, then choose to “Bake BODY Mesh Maps.”
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You’ll now have the mesh bake matching the vertex coloring for that specific material. Choose to view by ID if it’s not showing by default.
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Add a fill or smart material, then add a mask with color selection.
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Select “Pick Color” at the bottom, and then just pick the vertex color you wish to apply this fill/smart material to.
Now you can build a texture map the same as you would do in Blender or Godot or UE4 if you were using vertex colors.