Maya Alpha Technique

I have an animation question that's been killing me for years. I want to know if there is anyway to create an alpha type layer in maya to hide certain areas of geometry. A great example of what i'm talking about is the pixar short Presto: http://fliiby.com/file/62746/o34u18vx4k.html
There are objects going in and out of the hats and i need that exact technique to show proteins being made and ejected from the ribosome. Is this just crazy good compositing?