The two most important characteristics of any surface considered for wafer bonding are cleanliness, surface smoothness and macroscopic flatness. Silicon wafers in the as-received condition have a native oxide on the surface several nanometers thick [1], Figure la shows that they also have a layer of hydrocarbons. While they are not clean, they are smooth. Our wafers were plasma or ion cleaned, chemically treated, and ultra high vacuum (UHV) thermal desorption annealed in different combinations to find the best method for providing smooth, contamination free substrates that will produce an atomically flat, chemically clean Si/Si bonded interface.The first approach was a single step process to remove the contaminants and then bond the clean wafers. Cleaning was accomplished by ion bombardment of the surface in an UHV chamber with base pressure 1x109 Torr. This ion cleaning chamber is connected between the UHV (2x10-10 ) bonding chamber and UHV (1x10-10) analysis chamber, allowing wafers to be cleaned, analyzed, and bonded without breaking vacuum [2].