Try to find a good chemical etchant for SrRuO3, and see that it does not attact SrTiO3 as well. This can be a challenging search, but if you are lucky in finding a good etchant this will solve your problem.

Alternately,

You grind your STO substrate surface slightly, and re-polish it carefully. Since your used substrate are tiny enough, you need to hold them/embed them in a good mount which is sizable enough and allows you to hold the little tiny substrates you have. You may get some useful hints, how small samples are held in an epoxy resin while preparing samples for TEM or SEM microscopy.

Thank you all.