DEFORM-3D is a robust simulation tool that uses the finite element method (FEM) to model complex machining processes in three dimensions. One of the most recent processes that has been modeled in DEFORM is drilling. The program has many features that can be daunting and difficult to adjust for a new user. These features combine machining and the FE model to simulate drilling operations. Although this program can generate useful results, it can be very difficult to obtain these results consistently. This is because the code is often subject to crashing when the simulation parameters are not set properly. By recognizing the common errors and idiosyncrasies of DEFORM, a user can generate useful simulations quickly and efficiently. The background, application, troubleshooting, and analysis of DEFORM-3D are presented to showcase its capabilities while discussing its limitations in drilling.