AFM may not be a good option.. try TEM

Tried the HR TEM..cant even see the nanotube.

HRTEM is better to observe crystal structure of CNT

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)

http://www.youtube.com/watch?v=nXh5YXPYZq8.

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....