ERWin has this capability. ERWin can reverse-engineer an existing database into it's model. Afterwards you can have it compare the model against the database - or another database. This way, you can make structure changes to the database itself or to the model.

There is another ER modeling tool that has the same functionality, I don't remember which one. It was pretty recent, within a couple of weeks. Try using the search function and looking for ERWin.

-Mike