A method for processing substrates for a substrate processing facility includes the steps of: performing ventilation of a container with a fan filter unit while a lid of the container is in a closed state, when the container is stored in a storage shelf, and when the container is transferred with a substrate transfer device, and ventilating the container with the fan filter with the lid of the container in an open state, when substrates are transferred in a substrate loading/unloading section with the substrate transfer device.