The following pictures show the system I finished up about a month ago for holding BattleMechs. It will hold 21 'Mechs, with a two inch tall foam. The bottom of the box is a magnetic sheet. I am putting a piece of magnetic flexsteel (from Litko Aerosystem) to the bottom of each hex base.
View of the entire tray. The tray is 3" deep, and sized to fit my rolling aluminum case that my wife and sons got me for my birthday back in February.
Closeup shot of the 'Mechs in their snug little compartments.