I store my metal figs in one of those overpriced GW miniatures cases. And the foam still rubs the paint off, despite Clear Coat. I have to take them out one at a time, and carefully put them back when I'm done.
I store my prepainted plastic minis all together in a couple of those disposable Tupperware containers. I quickly root through the pile to find the figures I need for the game, and when the game's finished, I just sweep them all into the container, apply the lid, toss the whole thing into my backpack, and go.
I like my metal figs, and painting is fun, but boy, prepainted plastics sure are easier to *use*.
-z