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The best solution for nendoroid storage that I've tried so far. The box can be found at Michaels in the bead/jewelry section. I was really worried about all the painted parts rubbing against each other since it might damage the paint or lead to paint transfer, so I cut up the plastic that the nendoroids came wrapped in and used them as protective layers separating differently colored pieces.
[Edit]: I have four of these boxes filled after one year of collecting, and I'm now in need of a fifth. ´ ▽ ` )ノ