Hmm.... sounds like you need to do two things. If I understand it right your server has spawns and items in it that you don't want? I think you can just replace sphereworld.scp (in your sphere save directory) with a new sphereworld.scp file containing these lines:
TITLE=Sphere World Script
VERSION=0.55i //Or whatever
TIME=0
SAVECOUNT=1
[EOF]
That should get rid of all the moveable items. If you want to get rid of all the forests, buildings, foliage, etc, you need to find a way to clean out statics0.mul and staidx0.mul. I think it's both but at least one or the other (I'm not sure of the difference between these two files). Since you probably have dragon, maybe backup map0.mul and compile an 8x8 tile map or something? I think when you run dragonsp.exe it will clear out the statics and all that will remain, if anything, will be a couple items in the very northwest of your map in an 8x8 tile lol. Then replace your map0.mul and you should be ready. I'm sure this isn't the easiest way but works with what you have
-SnowCarve