Does anyone know what program was used to make this molecular structure picture?
The first type of image is very easy to make. I would suggest Avogadro with POV-ray. Avogadro can be used to draw the structures (or open a file containing the information, like .mol2, .sdf etc.) and then high-quality images can be generated using POV-ray.
To do this, install Avogadro, then draw a structure, and then File&gt; Export &gt; POV-ray. A new subwindow will open, where you can specify the location of the POV-ray executable.

In my case, the executable is pvengine64.exe, it might be different in different platforms, or in different versions.
You can also change the resolution here. Finally, click &quot;Render&quot;, and a new windows with POV-ray should open, and it should display the image, after a few seconds.

This is the image of the molecule that you showed in your question. The background looks like that because the &quot;Alpha transparency&quot; option is turned on in the Avogadro subwindow, which makes POV-ray render only the molecule, and there is no background.
As for the second picture, it looks like something that would be used in crystallography to represent probability ellipsoids of atoms. I don't know much about this, so I can't help you there.