The molecule they have been studying is called pentacene, a polycyclic aromatic hydrocarbon consisting of five linearly-fused benzene rings.
If you compare the previously known structure of the molecule (above) to the image seen under the microscope, the results are fairly spectacular. The new image clearly shows the bonds between the carbon atoms in the five linked rings, and even hints at the bonds to the hydrogen atoms around the edges of the carbon rings (these are usually omitted from the skeletal image above for simplicity).
The whole apparatus has to be extremely cold, at temperatures approaching absolute zero so as to avoid unwanted atom vibration, and the set up must be kept in a vacuum to eliminate stray molecules. You can read more about this by following the link below.
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