A system and method are provided for etching semiconductor wafers (integrated circuit substrates) with advanced packaging using a two-step wet etching process. The first etch step uses an etchant that is non-selective to at least the wafer material (silicon) and metals, such as copper and titanium, that are present in the wafer. The second etch step uses an etchant that is selective to the wafer material (silicon) and has low selectivity for the metals, thereby leaving them at least substantially intact.