Abstract: The present invention discloses a method to manufacture a self-aligned silicide layer on a substrate. A metal oxide semiconductor (MOS) device and a shallow trench are fabricated in the substrate. The device has a gate structure, spacers of the gate structured and doping regions. The shallow trench is refilled with silicon oxide material for isolation. A silicon layer is nonconformally deposited on the top surface of the gate structure, the spacers and the doping regions by using a physical vapor deposition (PVD) process, such as ion metal plasma (IMP) process. The IMP process, like a sputtering process, is to ionize a silicon material or a refractory-metal material to silicon ions or metal ions and the ions are biased to anisotropically deposit on the top surface of the substrate. A refractory metal layer is defined on the top surface of the silicon layer by the IMP technology.