So you already have deposited nanosheets on a substrate and you've already acquired a micrograph of the rim of the nanosheet, is that the scenario?

Then this "profile extraction" and "feature measurement" in Gwyddion (it's free) are what you're looking for:

http://gwyddion.net/documentation/user-guide-en/basic-operations.html

http://gwyddion.net/documentation/user-guide-en/feature-measurement.html

In most cases, you do not need any external software to find thickness from AFM. Just deposit a thin film or flake on a suitable substrate and keep a portion of it bare. Then take an areal scan (via contact/non-contact mode) and check the height profile through a line, where half of the area under investigation comprises the film, while the rest is bare. You'll get the thickness from the difference of average height of the two regions.

Dear Sajjad ul haq . See the following useful links: https://www.mdpi.com/2079-4991/10/3/526/pdf

https://www.google.com/amp/s/www.azonano.com/amp/article.aspx%3FArticleID%3D5960

Kindly see also the following useful links: https://www.mdpi.com/2073-4352/7/7/216/pdf

https://iopscience.iop.org/article/10.1088/0957-4484/27/12/125704/meta

Also check please the following useful links: https://www.sciencedirect.com/topics/physics-and-astronomy/atomic-force-microscopy

https://digital.csic.es/bitstream/10261/182473/1/Atomic_force_Paredes.pdf

The following RG links are also very useful: https://opg.optica.org/oe/viewmedia.cfm?uri=oe-30-4-4793&seq=0

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Aref Wazwaz While these are useful links, are you aware that you can post all of them in one post? That keeps the overview easier.

Dear Jürgen Weippert . Thank you so much for asking . Yes I can, but sometimes the answer can be from different angles (articles). The reader usually concentrate on the first answer ( article ) and ignore the rest . So if each answer alone, you can guarantee that all answers (articles) from different angles are read. Thank you so much. Wish you the best always.

Hi Sajjad ul haq

As Jürgen Weippert said, you can use the a method based on the relation of the z-dimensions of the substrate and the film topography images using the open-source Gwyddion software.

I let you a reference attached.

Regards.

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is there any document to find out the roughness of the film surface. I see many parameters like Ra, Rq, Rz in a table + there are green and red line profile and both have these Rz etc values.

Yes, sure. In Gwyddion there is the button "statistical quantities" down in the "tools" section, that's where you get these parameters.