In order to bake materials with multiple slots, you have to make sure that each material is assigned to a different island in your UV map with enough margin.

We will use for example Suzanne in this case with 2 procedural materials:

Once the UVs are ready we can assign a material to the object and then add a new slot (in the shader editor or in Sanctus Library panel):

In edit mode you can select the island that you want to use with the second material (you can select islands by pointing at them and pressing “L” in the keyboard), then with the SLOT 2 selected click the “Assign” button to assign that slot to your selection.

Now you can leave edit mode and with the SLOT 2 selected assign any other material to it

Now the baking process starts. First we add the sockets from the slot 1 to the baking queue (same as in the regular baking process):

Once added, switch to Slot 2 and use the PLUS button on the maps to add the correspond sockets of the second material (Color bakes with Color, Metallic with Metallic and so on):

Once you have all the maps paired you can adjust your baking settings and click bake:

And you now have the combined bake of the 2 slots in 1 material


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