if you are using version 1.x, the scene by default is transparent, so, when you create the flare3d scene/viewer - new Scene3D( container ), you can use as a container an empty sprite.
var sprite:Sprite = new Sprite()
addChild(sprite);
var scene:Scene3D = new Viewer3D(sprite)
....
in molehill version, you can not do that, because the stage3d is behind all 2d content.