To answer this question correctly, we need to be specific about the types of molecules being viewed. The reason is that while some molecules can be observed when they are viewed with microscopes, there are others that can't be observed by light.
For instance, a type of microscope known as an atomic force microscope can help view small molecules so much that you will be able to see the individual atoms that make up the molecules. On the contrary, you won't get the same result if you decide to use an atomic force microscope for single molecules.
Also, you won't get the same result for all types of matter. The reason is that the atoms of some matter are closely packed, while others are loosely packed. The type of microscope being used also has a lot to do with the result you would get. That said, you can always go for the one that will help you see the individual atoms.