Nihal Khatiwoda You may want to speak to a company that makes digital microscope stages that allow precise positioning. For example:
https://dovermotion.com/microscope-stages/
Alternatively, an automated image analysis system such as the Malvern Panalytical Morphologi 4 can automate your particle size characterization and will record the position of each and every particle so it can be re-examined. This is particularly useful with the Raman option the (Morphologi 4-ID) where a particle's chemistry can be examined with Raman spectroscopy. Also, if you want to return to do some confocal work with changing the z-axis this is very helpful. See:
https://tinyurl.com/5eyr2ppm
In this way you do not need to damage the particle in question. However, diamonds are routinely laser etched to mark significant details. I have no experience of this latter method.