JohnGames has made a Map Editor for Autonauts which you can find here.
Please note the map editor is a work in progress and may break/corrupt original game saves. That means it's highly advised to create an entirely new save.
If you think you've found a bug while playing Autonauts and have made changes to the save using this editor please also include in your bug report that you have used JohnGames's Map Editor.
Using the Editor Edit
With the editor you can Delete system32.