LabVIEW 2012 is shipping with a new API for manipulating icons. See <vilib>\LabVIEW Icon API. This would allow you to build up an icon in a layered way. However, the .mnu files still only store flat icons, so you wouldn't be able to get the layers back again unless you loaded them into the icon editor (which is possible... you would just need to create a temporary VI that has those layers and then ask the icon editor to edit that).