Install Bukkit (note: there is no 1.5 version out yet, you will have to wait possibly a week or more) together with WorldGuard and WorldEdit, and a permission plugin if you want to have several people do things what others cannot. If only you need to do special things, you do not need it.
with WorldEdit you can define a cube in the world and then use WorldGuard to define it as a protected region. Then you can add people to the region to allow them to edit it.
You can also simply deny building for anyone with the ModifyWorld plugin included in PermissionsEX and then allow then to build only in certain WorldGuard regions by adding them to that region. That has the advantage that you automatically prevent people building in the wild.