What year is your jeep? It'll depend on what seat you have. The more shallow early wrangler seat can easily be remounted from the floor to the top of an enclosure. The spring loaded (handle in the seat back later TJs) seat sits higher on metal runners. You wouldn't be able to have a very high enclosure (not enough airspace) and still have the seat in a normal position.
iPhone app user; excuse typos...thanx.