"Waves" is the right word. The problem is that the concepts that you are dealing with are confusing and cannot simply be expressed in everyday words. In fact, some people think that we simply cannot understand them in everyday senses at all. For more detailed ideas of the subject, you will have to work through writings on quantum theory.
Part of the problem is that on the scale of the size of atoms and below, there are two basic ways of looking at an object: as a wave packet of high frequency, or as an object. By looking at an object in the one way we affect its reality in the other way and we cannot measure it in both ways at extremely accurately. The more accurately we try to measure the position of the object, the less precisely we can measure its wavelength, and the more precisely we measure the wavelength, the more vague its position becomes.
I cannot put that more precisely here and now; you will have to read some material on quantum theory if you need to understand that.
However, some of the consequences of those facts about what things "look like" on the atomic and subatomic scale permit us to "see" various things about atoms, electrons and other particles, up to certain limits of accuracy or fuzziness in various ways. We can for example use field effect microscopes to "see" individual atoms and molecules under suitable conditions, and for the last twenty years or so, we can see a great deal more detail than before with the STEM (scanning transmission electron microscope) and since then with AFM (atomic force microscope).
Although there is some philosophical argument about whether we could call that "seeing" atoms, my personal opinion is that the question is a non-problem at practical levels. The short answer is that what we do looks very like seeing, behaves like seeing, and works like seeing. If anyone is to deny that it amounts to seeing, then he will have to redefine "seeing", rather than deny our definition of what such "microscopes" do as "seeing".
There is a great deal of written material on such subjects on line and in print, and I hope that what I have said can give you some idea of the basic ideas.