Dear Swarup, Atomic Force Microscopy (AFM) can provide you with valuable surface topography information including 2D and 3D surface micrographs together with high resolution height or depth profiles. Below you may find some examples of AFM outcome.
@Mahdi Ghamsari Thank you, sir, for your valuable suggestion. But AFM has one limitation it can capture a maximum area of 10*10 microns. Is there is any instrument capable of measuring the depth of the micro-patterns over an area of 5*5 cm2 rather than an optical profilometer?