I have modified Spiderweb Software's Blades of Avernum Editor (under the terms of its license).
I have added a powerful feature to the standard scenario editor: Editing in 3D, the way Blades of Avernum displays it. There are also a number of other improvements; see the readme file in the download.
This code is from 2005 and I have no idea if it still works; from the look of this Spiderweb Software forum, other people have since made their own more updated versions that you should probably use instead. Use at your own risk.