Abstract: An apparatus and system for wafer-scale microwave digestion of layers or structures from a large-scale semiconductor substrate include a digestion vessel with a chamber which is configured to receive a whole large-scale semiconductor substrate, such as a silicon wafer. The digestion vessel may be configured to be placed within a containment apparatus, which structurally supports the digestion vessel. A digestion method includes placing at least one large-scale semiconductor substrate within the digestion vessel with a polar solvent, placing the digestion vessel within the containment apparatus, placing the containment apparatus in a microwave oven or other microwave source, and heating the polar solvent and substrate with microwaves. The heated polar solvent dissolves one or more desired layers or structures and may be subsequently analyzed to evaluate the amounts of one or more materials of such layers or structures.