Well, almost anything that is solid can be analysed by AFM!
Here is a short list of SOME samples, in no particular order:

  • Polymers
  • Metals
  • Fibres: Hair, synthetic fibres, nanotubes
  • Particles: micro-, nanoparticles, quantum dots
  • Molecules covalently bound to a surface: e.g. self-assembled monolayers, and others
  • Molecules that are NOT bound to a surface, e.g. nucleic acids, proteins, many others
  • Minerals
  • Langmuir-Blodgett films, Lipid bilayers
  • Cells: Mammalian, Bacteria, Plant, etc.
  • Viruses
  • Ceramics
  • Plant surfaces: e.g. leaves, fruit
  • Paper

In short, if it has a surface, and it's solid, AFM can image it.
There has even been some work reported on gel and liquid surfaces.