Provided is a method and system for cleaning a substrate with a cleaning system comprising a pre-treatment system using an atomic oxygen generator. The substrate includes a layer to be cleaned and an underlying dielectric layer having a k-value. Pre-treatment gas comprising oxygen and an inert gas are delivered into an atomic oxygen generator, generating a process gas containing atomic oxygen. A portion of a surface of the substrate is exposed to the process gas while controlling two or more cleaning operating variables to ensure meeting two or more cleaning objectives and ensure completion of cleaning in the pre-treatment process time. In an embodiment, cleaning of the substrate in the pre-treatment process is set at less than 100 percent and a subsequent wet cleaning process is used to complete the substrate cleaning. In another embodiment, the pre-treatment system is configured to complete cleaning of the substrate.