Pipelines are a kind of terrain, they are indestructible tubes that supply power and raw materials to Black Hole's factories and cannot be passed through by any unit (not even air units can fly over them), except for a piperunner, which travels along them. According to some calculations, the pipelines are probably only 10 ft. tall, yet, air units cannot fly over them as part of the mechanics.
Although indestructible, they can be breached by destroying pipe seams. In maps without factories they only act as a barrier forcing a player to find another way around. In this case pipes are usually plentiful, located around entire bases with multiple seams to destroy. In factory maps however there is usually only one seam that must be destroyed to deactivate de factory and win the mission. Here, pipes are less plentiful or only located in one part of the battlefield.