A method of operating a wafer processing system includes etching a batch of wafers. The method also includes transferring at least a portion of the batch of wafers to a first front opening universal pod (FOUP). The method further includes purging an interior of the first FOUP with an inert gas. The method additionally includes transporting the first FOUP from a first loading port to a second loading port. The method also includes monitoring an elapsed time from the purging. The method further includes performing a second purging of the interior of the first FOUP if the elapsed time exceeds a threshold time. The method additionally includes cleaning the batch of wafers.