In this paper, a non-linear finite element framework was established for processing mechanics modeling of flip-chip packaging assemblies and relevant layered manufacturing. In particular, topological change was considered in order to model the sequential steps during flip-chip assembly. Geometric and material nonlinearity which includes the viscoelastic property of underfill and the creep behavior of solder ball, temperature-dependent material properties were considered. Different stress-free temperatures for different elements in the same model were used to simulate practical manufacturing process-induced thermal residual stress field in the chip assembly. As comparison, two FEM models of flip- chip package considered, associated with different processing schemes, were analyzed. From the finite element analysis, it is found that the stresses and deflections obtained from non-processing model are generally smaller than those obtained from the processing model due to the negligence of the bonding process-induced residual stresses and warpage. The values of the stresses at the given point obtained from the processing model are about 20 percent higher than that obtained from the non-processing model. The deflection values at the given points obtained rom the processing model are usually 25 percent higher than those obtained form the non-processing model. Therefore, a bigger error may be caused by using non-processing model in the analysis of process-induced residual stress field and warpage in the packaging assemblies. It is also noted that the viscoelastic property of the underfill considered in the flip-chip only cause 10 percent change of the stresses and deflections at given points at most. It is shown that the effect of viscoelastic behavior on process-induced stresses during the flip-chip assemblies can be negligible. The creep behavior of the solder balls has stronger effect on the normal stress and the peeling stress of the solder ball at the considered point. The steady state peeling stress is about 20 percent lower than the initial state peeling stress, while the steady state normal stress in x direction is only half the initial state normal stress in x direction.