A method and system for the megasonic cleaning of one or more substrates that reduces damage to the substrate(s) resulting from the megasonic energy. The substrates are supported in a process chamber and contacted with a cleaning solution comprising a cleaning liquid having carbon dioxide gas dissolved in the cleaning liquid in such amounts that the carbon dioxide gas is at a supersaturated concentration for the conditions within the process chamber. Megasonic energy is then transmitted to the substrate. The cleaning solution provides protection from damage resulting from the application of megasonic/acoustical energy. In another aspect, the invention is a system for carrying out the method. The invention is not limited to carbon dioxide but can be used in conjunction with any gas that, when so dissolved in a cleaning liquid, protects substrates from being damaged by the application of megasonic/acoustical energy.