We can easily plot intensity values of a SEM image as a surface. What is the relation of the contrast present in the SEM image to the actual height distribution of nano-structures? See the attached picture.
You cannot use intensity/contrast to make 3D measurements. Other technics do exist
http://literature.agilent.com/litweb/pdf/5990-9127EN.pdf
With tilt method (obtaining a stereo-pair) it is quite easy to make measurements and even calculations even with a ruler and a calculator. Also commercial software exists for these purposes (for example Alicona) with much greater capabilities.
Thanks for your response Prof. Vladimir. I would like to know in particular if I have the maximum height information of nanostructural architecture (some random morphology) through cross sectional SEM image and then I use that along with the top view SEM image intensity distribution. Is it anywhere close to the relative distribution of heights or completely incorrect. How much error could be there between the two?
As V. Dusevich pointed out, a simple correlation is still not yet convincing. The best way from my point of view is the use of several two and better more images from slightly tilted samples in order to calculate from the local shift the respective height. Then you need to have a calibration structures in order to reach a sufficient accuracy. The more images the software can handle the less artifacts you will have. Since all these programs (except shades of shading using backscattered electrons (BSE)) using cross-correlations between hopefully the same image details images without any characteristic and non-periodic structures cannot be used successfully. Moreover you need to take into account the signal formation of electron images. You have different electrons with different characteristic. Therefore, BSE s are less resolving. Secondary electrons of type 1 are the best with respect to the resolution. Nevertheless, it is an interaction of charged particles with a perhaps charging and conducting material. Especially along edges complex conditions exist which makes any interpretation of the visible contrasts difficult or even impossible. Combined with the limited accuracy of tilt stages the results are often not that precise and accurate as theoretically predicted and demonstrated on prepared shows :-). But for specific applications it helps if one can estimate and evaluate the critical parameters and errors.
In other words: it often sounds easy but if you need to do it by yourself you will realize that many things only theoretically work, and practically a lot of barriers have to pass.
Apart from the comments above, the following method using AFM (depth information) calibrated to SEM image reconstructs the surface.
http://link.springer.com/article/10.1186%2F2191-0855-4-3
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