The increase of surface microroughness on Si substrate degrades the electrical characteristics such as the dielectric breakdown field intensity (EBD) and charge to break-down (QBD) of thin oxide film. It has been found that the surface microroughness increases in the wet chemical process, particularly in NH4OH-H2O2-H2O cleaning (APM cleaning). It has been revealed that the surface microroughness does not increase at all if the NH4OH mixing ratio in NH4OH-H2O2-H2O solution is reduced from the conventional level of 1:1:5 to 0.05:1:5, and the room temperature ultrapure water rinsing is introduced right after the APM cleaning. At the same time, the APM cleaning with NH4OH-H2O2-H2O mixing ratio of 0.05:1:5 has been very effective to remove particles and metallic impurities from the Si surface. The surface microroughness dominating the electrical properties of very thin oxide films is strictly influenced by the wafer quality. The increase of surface microroughness due to the APM cleaning has varied among the wafer types such as Cz, FZ and epitaxial (EPI) wafers. The increase of surface microroughness in EPI wafer was very much limited, while the surface microroughness of FZ and Cz wafers gradually increase. As a result of investigating the amount of diffused phosphorus atoms into these wafers, the increase of the surface microroughness in APM cleaning has been confirmed to strongly depend on the silicon vacancy cluster concentration in wafer. The EPI wafer having low silicon vacancy concentration is essentially revealed superior for future sub-half-micron ULSI devices.