Input3D events are processed using the Stage. To filter the results, you can use Input3D.enableEventPhase. Using that, if some event was catched by another movieclip before reaching the stage, Input3D will ignore it. In the same way, setting it to false will make all events always reach Input3D (because they all reach the Stage).
But even if you have enableEventPhase set to false, you can always stop the event by hand. For example, if you have a 2d button, in your click handler you can do something like this:
private function buttonClickHandler( e:MouseEvent ):void
// your code and stuff
In general terms, event flow in Flash is a little convoluted, you can see more details here