If it's terrain based you were just unlucky with the placement of the terrain. You should be able to globally decrease the terrain height with the terraform editor but I've never had to do it so I couldn't tell you how. You may also be able to move the entire terrain down by moving the terrain block down but again, I have no idea if that works. Short of just remodeling all the terrain, you may just have to move the spawn point and let people build elsewhere. People expect buried bricks on terrain maps as long as it's not in a flat area.