Unfortunately I could not understand your question properly. However, if you are trying to measure the size of irregularly shaped nano particles using AFM, it may show a systematic bias in the size (usually smaller).

See the attached paper for more information

http://link.springer.com/article/10.1007/s00216-016-9909-x

Hello Ravikiran Attota Sir,

Thank you so much for your informative suggestion.

Sir I am asking about writing the discussion part after mentioning the result.

For example, If the average surface roughness of the sample is 7.4 nm. Then it would be the result but what should I write the in discussion section, means why the average surface roughness is 7.4 nm? 

and what would be the advantage of being such roughness?

Is there any relation of the average surface roughness and size of the particle?

and what more result can I extract from the 2D and 3D images?

Thank you sir..:)