A brush box cleaning module is introduced as part of the pre-treatment process flow in an integrated hybrid bonding platform. It addresses the technical problem of achieving high cleanliness levels on die front-side and back-side surfaces, particularly by removing residues and particles induced by backgrinding tape and dicing tape. The brush box cleaning module efficiently removes stubborn residues and particles both chemically and mechanically, resulting in a clean and passivated surface without causing watermarks, scratches, corrosion, or surface roughness. This disclosed approach enhances the bonding yield and provides significant advantages over existing methods in die-stack hybrid bonding applications.