You might need to switch out the stem, too, depending on the clamp diameter and bar diameter.

And your brake levers and MTB shifters might need to be replaced if their clamp sizes are different.

Try checking out Rivendell for info, they talked about switching bars and such in one of their Rivendell Readers.

Sounds like a fine idea, nobody says an MTB *has* to have a flat bar like every other MTB. Go for it!