While it's possible to build a model ship inside a bottle, the process is unbelievably difficult. So most bottled ships are built outside the bottle, flattened down, and then erected inside using a careful system of ropes (well, threads)—this is merely "very difficult." Watch Rob Morrison demonstrate the process, and think of how many ways this could go wrong and ruin all your work:

And here's a beautiful short film about a ship-in-a-bottle craftsman: