This article presents the development, verification, and validation of three-dimensional (3-D) numerical simulation for injection molding filling of 3-D parts and parts with microsurface features. For purpose of verification and comparison, two numerical models, the mixed model and the equal-order model, were used to solve the Stokes equations with three different tetrahedral elements (Taylor-Hood, MINI, and equal-order). The control volume scheme with tetrahedral finite element mesh was used for tracking advancing melt fronts and the operator splitting method was selected to solve the energy equation. A new, simple memory management procedure was introduced to deal with the large sparse matrix system without using a huge amount of storage space. The numerical simulation was validated for mold filling of a 3-D optical lens. The numerical simulation agreed very well with the experimental results and was useful in suggesting a better processing condition. As a new application area, a two-step macro-micro filling approach was adopted for the filling analysis of a part with a micro-surface feature to handle both macro and micro dimensions while avoiding an excessive number of elements.