A combined experimental and numerical studies are conducted to investigate whether the reliability of flip-chip solder interconnects are affected by the manufacturing induced defects (non-cleaning situations), in which underfill cannot be completely filled in the corners of the solder balls because contamination like flux residues subsist on those parts after solder reflow. The real-time moiré interferometry technique is used to measure the warpage for the selected “cleaning” and “non-cleaning” flip-chip package specimens during the test. A nonlinear finite element technique, in which the viscoplastic material properties (strain rate-dependent) of solder balls and underfill are considered, is adapted to simulate the corresponding “cleaning” and “non-cleaning” samples to assess the impact on solder interconnect reliability. The non-cleaning test and simulation results are contrast to the cleaning test and simulation results considered by many researchers. The results indicate that there is no obvious difference for the warpage obtained by either the test data or the numerical analyses between the cleaning samples and the non-cleaning samples. However, the simulation results of the stresses (strains) reveal that the non-cleaning situation decreases the mechanical stability and shortens the life time of those flip-chip packages to a level well below the predictions of the cleaning simulations. The fatigue life in some points of the outmost solder joint predicted by using the cleaning FE models is much higher than that predicted by using the non-cleaning FE models. Since it is hard to find perfect filled layers for any real world samples, the cleaning model yield overly conservative results. In addition, the predicted deformation values of the flip-chip package obtained from the finite element analysis are also compared with the test data obtained from the laser moiré interferometry technique. Good agreement is obtained. In particular, the displacement contours of the flip-chip package samples both in the x and y directions obtained from the test show similar distribution patterns compared with those modeled by the finite element method.