Dear A.S. Patil,

Although you have posted this question in 2014 almost two years before, I think you got the solution. However,  my answer might be helpful for others who need to do the similar analysis on plant wax. 

Firstly, one can take the SEM of the cross section of leaf (without destroying the wax layer). After that, you can measure the thickness by using photo analyzer tools like ImageJ. 

Kerstin Koch et al. measured the height by AFM ( for details you can check their publication)

Secondly, you can mechanically remove the wax layer by drying or freezing the leaf to get only the wax layer. Then analyze the wax crystals. For further details, I recommend you the below publication.

 Hope the above information will be helpful for your research. 

 Best Regards-

Habib

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