A scientist needs to take a picture of the well-ordered arrangements of the atoms and molecules within a substance. What instrument would be best for a scientist to use?

Answer 1

X-ray photography? "to take a picture" implies some sort of camera, wouldn't it?

Sra

Answer 2

X-ray crystallography, when the arrangement is well-ordered. There will be scattering in certain directions only, and the scattering pattern can be used with mathematical procedures to deduce the molecular and atomic arrangement in three dimeneions.

http://en.wikipedia.org/wiki/X-ray_crystallography

There are also new methods of tunneling scanning electron microscopy for imaging surface atomic patterns directly.
http://en.wikipedia.org/wiki/Scanning_tunneling_microscope