The difficulty of using focused ion beam (FIB) tools for embedded phase shift mask repair is the removal of gallium ion stain. Conventional anti-staining techniques, such as post-repair plasma etch or XeF2 assisted FIB sputtering, is not applicable to embedded phase shift masks because of the phase shifting error introduced by additional substrate etch. A novel techniques, focused ion beam biased repair, has been developed to eliminate the post-repair residual defects caused by gallium ion staining. The biased repair involves sputter removal of an opaque defect to an area larger than its original size. The reduction of light transmission due to gallium stain is then effectively compensated by the enlarged repair. The concept of introducing a bias is also extended for clear defect repair, which makes it possible to repair a clear defect by using simple FIB induced carbon deposition with no need to create a proper transmission and phase shift. The new technique has been confirmed by both computer simulations and experimental repairs of MoSi and CrON embedded phase shift masks.