Methods and apparatus for processing a substrate are provided herein. For example, a method for hybrid bonding a wafer comprises performing a first vacuum processing procedure on the wafer disposed within a first processing chamber, obtaining at least one of moisture measurements or organic species measurements within the first processing chamber, comparing the obtained at least one of moisture measurements or organic species measurements with a predetermined threshold, and one of when a comparison of the obtained at least one of moisture measurements or organic species measurements is equal to or less than the predetermined threshold automatically performing a second vacuum processing procedure in a second processing chamber different from the first processing chamber on the wafer, or when the comparison of the obtained at least one of moisture measurements or organic species measurements is greater than the predetermined threshold automatically continuing performing the first vacuum processing procedure on the wafer.