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I am working on this layout and find that it looks nice with a bit of Grease pencil on top... however you can see I am using a glass material and the grease pencil lines are not passing through. Does anyone know a fix to allow all the machinery behind the glass to be traced as well?

Thank you! enter image description here

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So I was able to come up with a fix after looking for a solution to this problem myself. Here's what I did and suggest you try :) if you hide the layer that isn't covered by the transparency you can bake the outline for that layer first, then unhide the layer that is above the transparency layer that you've baked already and add another grease pencil and bake for that layer too

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  1. You can also link your glass object into a Collection and set the Line Art Usage to "Excluded". Then the glass will not be used for Grease Pencil Outlines, and you can see through.

  2. Another option is to work with Occlusion layers, that were introduced in Blender 3.3.

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