30 minutes ago, IonThrust said:

Render side I'm not yet sure. Right now I disable the depth-buffer (or previously just set z to 0 in the Vertex Shader) when rendering the circles on top of the model so they're fully visible (and not partially inside the model). But then again I'd see all circles, even those behind the model.

Some things that might be good enough with depth test enabled:

Render spheres instead circles.

Pull the Circles a bit towards the camera (or use depth bias)

Render back faces of model and use that depth buffer for the circles. (This should be very accurate)