It is not possible to see atoms using an ordinary light microscope. One way scientists can determine the arrangement of atoms is by using x-ray diffraction. The same x-rays that a doctor uses to create a picture of your bones can be passed through other materials to help create a picture of the atoms that make them up. X-rays are electromagnetic waves with a wavelength of around 0.1 nanometers (1 nanometer = 1 billionth of a meter). Because the wavelength is about the same size as the spaces between atoms in a solid, x-rays get bent–or diffracted–when they pass between atoms. X-ray diffraction images of DNA taken by Rosalind Franklin were used to discover its double helix structure.
Check the links for more information on this topic.