You could put your air filter outside the body, if you fabricated a new intake duct that reaches to the carb. But you are inviting roost from other cars, and damage from rollovers to allow dust/mud/whatever into your engine.
If you do decide to make large holes in the body, I have seen many people who attach pieces of fine mesh to cover said body holes, that can help block some of the debris from getting a direct shot at your air filter element.