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This paper explores the lead-free (Pb-free) solder reflow process to achieve high assembly yield and solder joint quality for a 3-D silicon-on-silicon flip chip package. Three parameters, which included soak time, peak temperature, and time above liquidus (TAL), were investigated using statistical analysis to identify the nonlinear effect (quadratic effect) of each factor as well as the interactions among the factors. Different reflow ambient gases such as air and nitrogen were investigated to understand the sensitivity of the yield under ambient gases. This paper also revealed that 100% assembly yield can be achieved with a wide process window on the structured silicon-on-silicon flip chip package under nitrogen reflow environment, by investigating 15 reflow profiles designed following the response surface methodology. Within the reflow process window, the solder joint intermetallic compound (IMC) thickness was measured by calculating the average IMC thickness using a mathematical integration method. It was concluded that an increase in TAL results in an increase of IMC thickness.