The recent progress of advanced millisecond annealing (MSA) technology is discussed for the application to the advanced logic LSI fabrication processes. The combination with conventional spike annealing and MSA is proving practical to reduce the parasitic resistance and control the dopant diffusion. The characterization result of advanced 45 nm generation devices including the channel straining technology using embedded SiGe epitaxial growth is described with the arrangements of process flow and annealing steps. MSA has a principle problem of the annealing temperature variation depending on the optical properties of materials on the wafer surface because the annealing process time is similar to the heat transfer time. In the device scale, the variation of temperature is examined as the exact temperature with newly proposed evaluating methods used for the first time in this industry.