One of the best ways is to actually put on a coat of gloss varnish first. It will dry with a hard outer surface, follow that with any number of matte coats to get rid of the gloss. That should protect your mini pretty well.
I view my min's in two ways. It is either a tool or a jewel. The "tool" mini's tend to be the plastic mini's that are stand infantry, while the jewels are the metal ones. This is not always the case but it generally holds true. Tools get put into storage any which way, jewels are carefully placed standing up, or if they are too tall they are placed on foam or paper towel.
Another thing to help paint stay on, get a good even layer of primer, not too think and not too thin. Make sure it is a primer for metal if you are using generic primer form a non-game store.
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