I'm trying to do a whac a mole animation in After effects, but i'm not sure how to approach the holes they rise out of. Similar to this. I'm trying to make it look like the mole is actually going inside the hole layer, without it showing around the actual hole. I hope this makes sense.
You set up a layer above the top cut out to fit the bottom of the hole above the layer with the animal and use that layer as an Alpha Inverted track matte. This series of screenshots should help. The basic scene: