The practice that is required to use the AFM, its software, and the user manual to perform calibrations for the instrument is the starting point that you seek. Read and follow standard, generally well-documented protocols that explain how to confirm sizes and thickness values from features on well-defined substrates such as the calibration standards that come with AFM instruments as well as the heights from well-defined edges such as those on mica. In parallel, search for literature that explains how others have mounted and analyzed MoS2 samples with AFM. Google Scholar gives a host of references with just the words "afm, mos2". When you do not have at least this level of hands-on experience and literature background, we have no basis to explain anything to you well enough to know that you will truly understand.

I use Gwyddion to make measurements from my AFM images. It is a free software for AFM imaging. You can find it by doing a google search for "gwyddion" and it is the first link to come up. Once you open the image in Gwyddion, you will need to process the image. For example, you may want to remove a background or doing some leveling. To make the measurement, do a line scan. From there, you can make height measurements about the topographic features you are interested in.

Let me know if that doesn't make sense or if you have other questions! Good luck!!

Meagan