Provided is a method and system for cleaning a substrate with a cleaning system comprising a pre-treatment system and a wet clean system. One or more objectives for the pre-treatment system are selected and two or more pre-treatment operating variables including UV dose, substrate temperature, oxygen partial pressure, oxygen and ozone partial pressure, and/or total pressure, are optimized to meet the pre-treatment objectives, using metrology measurements. The substrate includes a layer to be cleaned and an underlying dielectric layer having a k-value. A pre-treatment gas comprising oxygen and/or ozone is delivered onto a surface of the substrate and irradiated with a UV device, generating oxygen radicals. Cleaning of the substrate in the pre-treatment process is set at less than 100% in order to ensure the change in k-value of the substrate is within a set range for the substrate application.