IBM has made a stop motion animation by moving individual molecules. Ars Technica has an article about it here.

You're about to see the movie that holds the Guinness World Records™ record for the World's Smallest Stop-Motion Film (see how it was made at http://youtu.be/xA4QWwaweWA). The ability to move single atoms - the smallest particles of any element in the universe - is crucial to IBM's research in the field of atomic memory.

Animating Atoms