it is hard to get atomic resolution with AFM, but possible. This lecture may help (Lecture 23: FM-AFM Selected Results and Achieving Atomic Resolution with AFM)
We have done similar kind stuff. We had a wrapping of some hydrophobic molecules on carbon nanotube. If you can deposit them on AFM grade mica before and after polymer wrapping. You can observe some change in height. Though I would advice you should use softer cantilever and try to image at low drive amplitude. I hope this helps....