Have only certain meshes visibile through transparency?

That’s the classic problem with alpha blended meshes, because they don’t write to the zbuffer. See Transparency and How Meshes Are Rendered - Babylon.js Documentation for more detail.

Alpha blended meshes are sorted before being rendererd, but the faces inside a mesh are rendered in the order of their creation, except if you use the facet depth sort (see previous link).

In your case, as there is nothing behind a cloud, using material.needDepthPrePass = true should work.

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