You could take a look at an engraving pen:
Image courtesy of Amazon
They're like a pen shaped hand held drill, with a fine tip that is diamond abrasive coated. If you lightly make some marks in the case it should be more resistant to degradation from insertion than eg Liquid Paper is
The casing on a MicroSD card is quite thin; don't go too deep. There are a few videos and images around the web of what's inside an SD but there wouldn't be any substitute for taking one of your old dead ones and sanding the case off to find out where it is thickest/where you wouldn't hit any circuits.
Image courtesy of YouTube video "Checking out and watching mind blowing technical design Inside of Micro SD Card
From what i've seen it looks like the best place to grind a few little dots might be the edge that you insert into the holder, on the opposite side to the gold contacts, so that your grindings don't interfere with (bend) the spring contacts on the socket, but there is also a ticker part of the card where you grab it to pull it out, that might just be a lump of plastic with no raised components inside
a coding system that is like binary will count to 8:
Width of sd card
##################### - card 0
#####################
############### ### - card 1
#####################
######### ######### - card 2
#####################
######### ### ### - card 3 (2+1)
#####################
### ############### - card 4
#####################
### ######### ### - card 5 (4+1)
#####################
### ### ######### - card 6 (4+2)
#####################
### ### ### ### - card 7 (4+2+1)
#####################
If you don't want to lay out on an engraving pen (probably about $10) you could try a nail file for this applicaiton.. but when yu have an engraving pen they are useful for all sorts of things. Worthy purchase