Here is the best way you can do this:
• Open your world using MCEdit and select the whole area you want to save. I suggest you to keep a bit of unmodified ground around / below.
• Use the export tool to make a schematic out of it and save it somewhere easy to find.
• Log into your world and type
/seed to get the seed of the world.
• Create a new world using that same seed.
• Open this new world in MCEdit, use the import tool, and find the location of the saved schematic.
• Place it at the exact same position using the unmodified ground you selected previously.
• Save.
• Upload the new world to your server
You can download MCEdit
here if you don't have it yet, and find a simple basic tutorial
here.
Hope that helped!
~Ama
