Here you have both vertical and horizontal negative cylinders creating holes in a positive terrain. Materials transfer from the boolean object is turned off. If you followed the steps correctly, including grouping the positive and negative objects together the process should work. If it doesn't, I suggest you start from scratch. Perhaps you duplicated the terrain unknowingly. That would cause a problem like the one you're describing. Good Luck! : ) (PS- Make sure that the negative shape is large enough to extend entirely through the positive shape)