Help you delete unnecessary trunks.
java -jar mmat.jar -w <world path> [-d <dilation size>] [-p <id list>] [-r <minX,maxX,minZ,maxZ>] [-y <yBegin,yEnd>]
Where:
-w <world path> Path to the world folders
-d <dilation size> Dilate preserved area to perserve more chunks around the chunks with "perserve block".
-p <id list> Define a list of "perserve block".If a chunk contains any "perserve block", it will be preserved.
-r <rect> If specified, all the chunks outside this rectangle will be forced to delete.
-y <yBegin,yEnd> If specified, only scan this range of height.
Examples:
java -jar mmat.jar -w ~/minecraft/world
java -jar mmat.jar -w ~/minecraft/world -d 3 -p 63,68 -r -1000,1000,-1000,1000 -y 64,256
http://forums.bukkit.org/threads/tool-admin-minecraft-map-auto-trim-v0-2.37846/