A system for cleaning a container such as semiconductor wafer carrier includes a housing, a cleaning unit in the housing, an analyzing unit within the housing, and a vacuum unit within the housing. The cleaning unit comprises a cleaning chamber, and is configured to spray a cleaning medium into the container in the cleaning chamber and dry the container. The analyzing unit is configured to analyze air inside the container coming out of the cleaning chamber, and provide a testing result for each ingredient of possible airborne molecular contamination (AMC) and humidity. The vacuum unit comprises a vacuum chamber configured to apply vacuum onto a container when the testing result for an ingredient is higher than a respective threshold.