In Gwyddion, there are some tools for grain analysis. Please check out if one of them matches your situation:

http://gwyddion.net/documentation/user-guide-en/grain-analysis.html

Thank you Dr. Jürgen Weippert for you kind reply.

All those methods have been used. But due to several variations between the results from different methods, I am finding for the accurate one from the experiences of the researchers.

Thanks again.

The best way to finding the right method for your specific substance is probably checkinf 2-3 images "by hand", so you determine grain sizes by manual choice and then check which of the automated methods comes closest.

Id recommend ImageJ. It's a pretty powerful analysis tool. If you set appropriate thresholds the software will do the heavy lifting for you.

One aspect to bear in mind is that the finite size of the AFM tip can matter if your grains are relatively small. That is, in the measured images the grains will appear wider than they actually are if the radius of the tip apex is similar to the grain diameter, or even bigger. In the opposite case of a tip radius much smaller than the grain diameter (eg, 5nm tip radius vs 150nm grain size), this dilation effect should be negligible. To get an idea of the tip size, you might like to image nanoparticles with a narrow and well-known size distribution. To check for potential tip wear, such reference measurements could be run before and after the actual imaging of the grains. Good luck!

Thank you Mr. Martin Munz for your kind and informative reply.

Thank you Mr. Adam Weidling for your important suggestion.