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Three-dimensional (3-D) stacked die packaging can reduce cost and improve performance. It utilizes the oldest process, wire bonding, to connect chips with a large bond height difference (BHD) via deep cavity looping. This paper develops 3-D and 2-D finite element models of the process and validate them against experiments. The effects of the height difference between two bond points, reverse motion parameter, kink height parameter, and elliptic capillary traces on the process are studied. The simulations demonstrate that deep cavity looping produces greater deformation on kink II, a lower loop height, and more violent pulling on the wire than traditional looping. Optimized capillary trace parameters for traditional looping are not suitable for deep cavity looping; however, the trends in the effects of the parameters are the same. Elliptic capillary traces can change wire profiles significantly.