you mean the surface roughness inside, like at the bottom of the hole? or the wall surface? or the top surface? what size hole are we talking about?

@Virginia Claudio

Yes, surface roughness on the internal wall surface. Size of microhole is 0.1 mm.

i think there's no other way then cutting a section with a precision diamond blade, have your substrate previously marked by reference marks every say 1 mm, and look at it with SEM. after you know you have caught a few holes at least in your section, mount it perpendicular and check it with AFM. another way could be light scattering, depending on the material. But you would need some sort of reference in the same material for calibration.

@Virginia Claudio

Thank you for the reply.

Is there any alternative other than SEM or AFM for knowing the surface roughness?

Could you elaborate on the light scattering?

If your hole is more than 100 um wide, cut it precisely through the middle of hole with the help of a diamond wafer cutter, use a Zeta profilometer to measure the roughness. Make sure that you are mounting your sample perfectly vertical. If you need precise measurement of roughness, you should use SEM or AFM.

@Jose Joseph

Thanks

you can try stylus profilometer for measureing the surface roughness in the hole...if the hole depth is not too much....

@Shankar Dutta

Sir, Can you elaborate on this as the hole diameter is 0.1mm and depth around 10mm?

I think stylus of 0.1 mm dia. is not available.