"Copper plate: The scientists used copper 111 as the surface of the animation — the same material they used 10 years ago when they built the first computer that performed digital computation operations. Carbon monoxide (CO): ok The scientists chose carbon monoxide molecules to move around the plate. Carbon monoxide has one carbon atom and one oxygen atom, stacked on top of each other."

http://www.research.ibm.com/articles/madewithatoms.shtml#fbi...

I assume focus / depth of field is why the surface looks smooth. Or whatever the equivalent of that is for a scanning/tunnelling microscope.