Dear Dr G. Kiruthiga , to calculate thickness by FESEM you just need to measure the thickness of the object of interest in the FESEM image, using the escale bar that appears on the FESEM image (normally).
To measure thicknesses of say layers in a specimen, it is necessary that these layers show a clear border or enough contrast to be able to make the measurement. Often, the software of the FESEM allows you to make measurements while you are taking the picture, and you can even leave a measuring mark or label on the image (or several, for example, if you have three layers, you can leave a thickness measurement for eachone.
If both stylus profilometer and FESEM are properly calibrated, they measurements must be comparable.
Sometimes your FESEM image could show your sample somewhat tilted, in this case the measurement would be more complicated. If your are doing this live, you can change the orientation of the sample so that the thickness of the object to measure will be orthogonal to the beam, in this case the measurement will be easy.
Sometimes we forget to adjust the FESEM´s software settings relative to the scale bar, so it doesn´t appear on the image. This is a problem when you want to do measurements over that image. Sometimes you still have some data like the magnification (on the image itself or as some information on the image file), but using this value es not direct and mistakes can happen, causing the lack of matching with other measuring systems like the profilometry. It is good practice to activate the scale bar always, or if not, asking the microscopist that include it in your images, so that you can use it to get real measures of your specimen.
When you want measure the thickness of layers without contrast between them, you can try to change the microscope detector, and this still doesn´t work, you can visualize layers differences by mean of EDS if the layers have different atom compositions.
You should mount your sample first using mounting press machine to fix the alignment of it. Then polish the mounted specimen across the cross-section of it using grinder-polisher machine with different grade of SiC papers and continue the polishing process until the polished side looking like mirror. Then apply the appropriate etchant ( For 300 series stainless steel you can use carpenter) for 3-4 seconds to remove the chip and burr on the polished side. After that, you take images from the cross-section side using either SEM or FESEM. In the image, you will have a scale (for example 20 micro-meter). You can measure the coating thickness based on the scale. You just need to imagine the scale along the Y axis to measure the coating thickness. Easy to measure it. Good luck. Please, you will find relevant published papers in my profile. Please visit and request for the papers.