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I know that this question has been asked a LOT of times before, but none of the answers suited me, so...

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This is a mesh with glass material applied. And everything is perfect. I can see everything through clearly (just a UV Sphere behind mesh).

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But when I add "liquid" inside, with the same glass material applied, it is not transparent.It is on the other hand transparent when i hide the cup, but when it is looked through the cup, it is not.

enter image description here I use cycles, and I tried to tweak everything, but with no luck.

I would not like to reset blender to default, because I have startup file finely tweaked.

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This appears to be because of overlapping faces. That is, two faces being in the same position. I cannot guarantee this is the case, but two transmission materials overtop of eachother sounds fragile.

I recommend either scaling the liquid block down slightly, or doing the following to change the liquid setup:

Make the separate liquid object just the surface. Change the underwater part of the glass to a liquid-colored material that has a refraction index so as to match light going from glass into water as opposed to leaving air. You could probably get away with subtracting the IOR of glass from that of water, then adding 1. For a more accurate result, I'd have to think about the math, here's the law: https://en.wikipedia.org/wiki/Snell%27s_law If you aren't sure what to do, I might could look into it.

Hope this helps :D

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