S.E.
My son was a micro machine nut when he was young.
We used small tackle boxes to separate and store all the tiny cars and star wars micros. In fact at age 18 he still has all of his micro stored away for his children to have one day. (Hopefully years down the road) See the link for an example.
http://cgi.ebay.com/Plano-Utility-Tackle-Box-ProLatch-Sto...
http://cgi.ebay.com/Soft-Sided-Tackle-Bag-w-4-Plano-boxes...
http://cgi.ebay.com/Plano-Tackle-Box_W0QQitemZ16027231554...
if you live near Plano, IL, Plano molding has an outlet store that they sells there overstock at. Can buy cheaper than at Wal-mart.
He also has some small lunch boxes holding some of his duplicates.
Good Luck,
S.