Silicon wafers are used to fabricate more than 90% of integrated circuits. Surface grinding has been used to flatten wire-sawn silicon wafers. A major issue in grinding of wire-sawn wafers is that conventional grinding cannot effectively remove the waviness induced by wire-sawing process. Soft-pad grinding is a promising method to effectively remove waviness. This paper presents the results of three-dimensional (3D) finite element analysis of soft-pad grinding of wire-sawn silicon wafers. In this investigation, a four-factor two-level full factorial design is employed to reveal main effects as well as interaction effects of four factors (Young’s modulus, Poisson’s ratio, and thickness of the soft pad, and waviness wavelength of the wafer) on the effectiveness of waviness reduction. Implications of this study to manufacturing are also discussed.