Dear Ozyegin

At the spatial resolution of the AFM, at nearly atomic resolution, all surfaces are flat. In other words, the surface roughness of etched wire- shape sample requires no special method in order to perform AFM tests. Please refer to the attached article.

Dear Gorkem,

I suggest you use SEM to see the surface morphology of the wire. You can at least see the nature of etching. I am not sure if a normal AFM will give you any reliable data.