Guys, there is a tool in the FS9 Autogen SDK called "autogen annotator". I don't have access to my refs right now so can't give you the specifics, a Google search "autogen sdk" should turn up some info on it.
Java
Yep, here's one at the SHOF (Scenery Hall of Fame)
http://www.scenery.org/tutorials_fs2k4_SDK.htm
The Autogen Annotation tool enables you to edit or create annotation files for both generic and unique terrain textures. This tool opens .bmp files and allows you to place footprints for objects on the image file and to set certain properties for those footprints. Autogen then uses the annotation files to display 3-D objects (buildings and vegetation). No prior programming experience is needed to use this tool.