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Flip chip solder joints are one of the major interconnection methods for IC packaging. In many micro-electro-mechanical system (MEMS) applications, flip chip solder joints are used due to their self-alignment feature and their superior electrical performance. The requirements for positioning precision in certain MEMS applications are very tight. The overall performance of the system may be affected if there is a slight misalignment in some directions. In general, the lateral position of the component can be easily defined by the bond pad locations. However, the determination of the vertical position, which is related to the solder joint standoff height, is not so straight-forward. Although there are several prediction methods available in the literature, most of them are complicated and lacking experimental validation. Moreover, the effects of key parameters are not clearly identified. In the paper, an innovative numerical prediction model is proposed. The targeted application is a MEMS microphone with a 3D flip-chip-on-chip package structure. In order to maintain a certain gap space between the MEMS microphone chip and the package substrate for the intended acoustic function, the final standoff height of external solder joints between the silicon chip carrier and the organic substrate is very critical. Experimental data shows that the proposed numerical model is very useful and effective in predicting the final solder joint standoff height during the design stage.