I'd say it's 3D in the sense that it's a height map rather than a cross section. (We've been able to see cross-sectional images of bonds for some time using transmission electron microscopy, I think). It's not a full three-dimensional structure though, and it'd only work on flattish molecules like this.
It should be noted that this sort of resolution has been attainable for some time using scanning tunneling microscopy, but I'm pretty sure this is a first for atomic force microscopy. STM doesn't give you a very good image of bonds -- in fact bonds are generally the thing you _don't_ see, since STM works by pulling electrons in/out and bonds are stable places where electrons really don't want to come out of or go into. AFM, on the other hand, shows bonds very nicely.
You can sorta make out where the aromatic rings are. I'm not sure why it's so bright at the ends -- any organic chemists out there who can explain that?