A novel silicide process with two-step low temperature microwave annealing (MWA) achieves NiSi thickness of 10 nm while maintaining low resistance, and an ultra-thin Ni silicide film, only 4.5 nm, has been realized. In this MWA system, we insert quartz and Si susceptors to change the absorption efficiency of the process wafer and provide fine turning in temperature control during annealing. The thickness of NiSi film is determined by microwave power and by changing the number and the position of quartz and Si susceptors in the first step of the anneal process. The STEM-HAADF combined EELS/EDS spectroscopies are used to analyze the electronic excitations and identify the phase of Ni silicide.