The laser light is absorbed by the atom and is released at a different wavelength. While the radius of the atom is 200 x 10^-12 meters, the wavelength of the light being emitted is in the visible spectrum, so between 380-500 x 10^-9 M which is why it is visible at the scales you can see.

A scanning electron microscope, or an x-ray crystallography based machine, uses items with much smaller wavelengths, .01 - 10 nm in the case of x-rays and so they're able to peer inside an atomic structure.