Embodiments of an apparatus and method of monitoring and controlling a large area substrate processing chamber are provided. Multiple types of metrology tools can be installed in the substrate processing system to measure film properties after substrate processing in a processing chamber. Several number of a particular type of metrology tools can also be installed in the substrate processing system to measure film properties after substrate processing in a processing chamber. The metrology tools can be installed in a metrology chamber, a process chamber, a transfer chamber, or a loadlock.