Masking With Vertex colors - TehMerow/PBR_Bake_Tools GitHub Wiki
Currently, one button baking with multiple materials on a single object is not possible with this add-on.
However, it is possible to use multiple texture groups within a single material and then mask those with vertex colors
It is also possible to connect the PBR Bake nodes outputs to the material output in each material on the object, have the same output textures in each material and bake that way.
The process
Vertex paint
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Open "Object Data Properties" under the properties panel, expand "Vertex Colors", create a new Vertex Color and rename it
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Go into "Vertex Paint" Mode in the viewport and activate "Paint Mask" in the top left corner of the viewport or press "m" on your keyboard
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select all and set the vertex color to black
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Deselect all the faces and then start selecting each face you want to have a different material on
Node Editor
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Open up the Material in the node editor and add your textures
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Select 2 of your Base_Color Textures and combine them with a MixRGB mode
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Add a Vertex Color node, select the Vertex Color mask and connect the vertex color output to the mix factor of the MixRGB node
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Continue for roughness,metallness etc
If you have more than one 'material' keep mixing them with MixRGB nodes and different vertex color masks