I don't know if it will work for an egg that small, but with normal size eggs, I put a hole in the top and bottom with a skewer, and put it to my mouth and blow, and all the insides come out, then I run water through it to rinse.
One of my EE's laid a little green one like that the other day. I handed it to my DH and said, "Here, Eleanor made you breakfast today." It's a cute little thing. Do they have a yolk in them when they're that small?