Most drop handlebrs have a larger diameter clamp surface than most road bars. That means that, when you replace the bars, you'll also have to either replace the stem or to use some kind of shim. I'd suggest replacing the stem because you will probably want a shorter one with a little more rise anyway. Besides, it makes for a cleaner conversion.
You will also have to replace the brake levers and shifters. I've had good luck using mountain bike rapid fires with road front derailleurs, but now Shimano has a shifter that's designed to do that. Cable routing going from a road bike to flat handlebar won't be a problem.
If you have road caliper brakes, you will probably be limited to 28mm wide tires. Otherwise you'll have to deflate your tire everytime you want to remove a wheel because it won't squeeze past the brake calipers.
If you do a workmanlike job and are careful with your selection of components, there's no reason why this type of conversion can't look "factory."