X-ray diffraction, atomic force microscopy imaging of single molecules, anything?
I was tempted to use the title Has anyone ever seen a nanoputian?
Edit: The IBM video World's Smallest Movie is not of a molecule, but it does contain an anthropomorphic shape built from individual atoms, visualized at atomic resolution using scanning atomic force microscopy.
below x2: Simple illustration of AFM imaging of organic molecule shape. From here. For more recent experiments and videos, see 30 years of atomic force microscopy: IBM scientists trigger and observe Reactions in an individual molecule and also IBM & Warwick Image Highly Reactive Triangular Molecule for the First Time.
below: Lewis structure of a nanoputian; "Chemical structure of 2-(2,5-bis(3,3-dimethylbut-1-ynyl)-4-(2-(3,5-di(pent-1-ynyl)phenyl)ethynyl)phenyl)-1,3-dioxolane." From here.
below: Lewis structure of a nanoputian; "Ball-and-stick model of the nanoputian molecule, also known as nanokid, an synthetic compound whose molecules are human-shaped." From here.