Biology is organized in a hierarchical system. From largest to smallest, the list would go something like this:
For more detail on what each level is comprised of, see the link below.
Generally speaking, most microscope work is done at the tissue, cell, or cell organelle level. Molecules are usually too small to be studied with a microscope. In order to do research at the molecular level, scientists have had to devise a variety of techniques, including tagging specific molecules with radioactive isotopes, separating molecules via electrophoresis, western blot, or chromatography, or doing spectroscopic analysis.
The science of biochemistry is entirely devoted to studying the chemical reactions carried on by living cells; biochemists are therefore working at the molecular level. It is a fascinating field requiring a lot of theoretical knowledge, as things must be studied indirectly rather than by direct observation.