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I am making a character for a game in Unity. It is supposed to be animated and textured later and I want to follow best practice in the creation process. I don't know which way to make the eyes of the character. I started with knife projection, but figured this would create ngons. Then I've seen people just making spheres inside the mesh like this:

enter image description here

But wouldn't this make the mesh either non-manifold (holes between eyeballs and socket) or intersect (also they eyeball and edges of socket)? Isn't that bad if you want to follow best practice? What options are there? What is the preferred way?

Is making the eyesockets manifold and then placing an eyeball inside that carving an option (hard to make it blend with rest of the face though)?

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It won't be non-manifold ; a manifold mesh can have holes.

It will intersect, unless you make sure the socket contour is perfectly adjusted to the eyeball (you can use surface snap, or maybe a shrinkwrap modifier). Intersect isn't really an issue in the vast majority of real time engine ; in fact, it's often used to save up polys.

An other technique is to model only the visible part of the eye (make the eye a bump in the face, like a statue or a sculpture) ; and use a shader trick to move the pupil. You can find many eyes shaders in the asset store.

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