There are three kinds of rooms that you need to clear out before you can build over it.
Alien Debris - This is the quickest to clean and provides miniscule amount of supplies. These supplies are random in numbers and in type. Every playthrough has different value and resource to be harvested off these rooms.
Alien Machinery - This takes a little bit longer to clear out, however there should be alien alloys included in the reward. Significant amount of supplies are also there for the taking.
Exposed Power Coils - When there is only one Engineer clearing out, it should take 30 days for the room to be cleared out. A room with exposed power coils is best for those Facilities that requires a lot of power and has upgradeable systems like the Psi Lab, Shadow Chamber, and of course, the Power Relay. The Power Relay when built in a room with exposed power coils will have extra power to boost your other facilities.