Abstract: A method for forming a hydrophilic surface on a silicon substrate during cleaning step after well implantation comprises providing a silicon substrate and an insulating layer is deposited thereon for mask alignment requirement. A photoresist layer is formed on the insulating layer and then a well pattern is transferred into the photoresist layer to expose partial the insulating layer thereunder the well defined. Next, implants are implanted into the photoresist layer, the insulating layer and the silicon substrate. Then the insulating layer exposed by the photoresist layer is removed and in-situ a native oxide is formed on the silicon substrate thereunder the well defined whereby changes the surface of the silicon substrate from hydrophobic into hydrophilic. A hard skin on the photoresist layer, resulting from implantation, is removed by oxygen plasma ashing and then the surface of the insulating layer and the silicon substrate are cleaned by conventional technologies.