When I was a lad and my brother was on the medical school track in college, I remember he had these plastic models that he used for his organic chemistry class. I remember remarking that, since he got to play with cool little plastic models, it must be a fun class. He tried to persuade me otherwise.
I always had a soft spot for those molecular modeling kits. But still, it’s hard to escape the feeling that maybe it’s all a big humbug. In chemistry class they tell us what these things look like, but honestly, what do they REALLY look like?
CHEMISTRY PROF: You can’t “look” at molecules.
STUDENT: So why am I fumbling with these expensive goddamned plastic noodles?
The message is, trust us, they look like this, but you’ll never see them.
Except for the fact that now you can. Starting with the scanning tunneling microscope, we’ve been able to resolve shapes down to the atomic level (note that I am going to sidestep any philosophical concerns about whether using an atomic force microscope constitutes seeing). It’s very satisfying to see what Democritus dreamed of.
Recently the level of detail has gone way up. Look at this image of pentacene, which is a kind of stretch-limo version of benzene. Here’s the ball and stick model of the same thing. By god, it REALLY looks like that plastic model. I am going to sleep well tonight.
Rambles Blog at Star Chamber 
I was lucky, in that my high school chemistry teacher gave a more satisfying response by blaming mathmaticians and physicists for coming up with all of the weird electron clouds and orbitals using statistics. His explanation was more: we can’t entirely explain why molecules look like that, but we have enough evidence to know that they would if we could see them.
Now if they can just upend the darn thing so we can see the pi-orbitals!
Next on the visualization agenda: economics. I want an X-ray machine that can show me Adam Smith’s Invisible Hand.
I think you need Kirlian photography for that.