Pile Bunkers are rod-like objects driven into the ground to suppress the tectonic shifts in the Scub Coral, which otherwise cause huge, mushroom-like coral formations to erupt from the ground with little to no warning. They often don't do anything, but may even make matters worse, as shown by Martha and William B. Baxter.
In Eureka Seven vol.2: The New Vision, it is shown that the pile bunkers are produced, and dispensed through the flying fortress, Thundercloud. Thundercloud moves all throughout the planet dispensing pile bunkers to keep the protruding coral formations at bay, although, this has made Thundercloud a target for the UF's enemies as it can instead cause great damage by firing the pile bunkers in populated areas instead.