Numerical manifold method (NMM) has shown its ability to solve continuous and discontinuous deformation problems in a unified framework. However, due to the complexity of geometry description and the absence of a reliable 3D contact algorithm, the development of 3D-NMM still has a long-time challenge. In this study, an open-source software named MEG3D to generate the numerical model for 3D-NMM is developed. The MEG3D is a fast, light, and user-friendly interactive software to identify geometry, generate joint networks, generate structured finite mathematical mesh, cut blocks, and generate numerical manifold elements (MEs). In this software, a new C++ programming strategy with high modularization and good portability, and a novel data storage format and data structure were used. Based on the OpenGL library, real-time visualization and interactive interfaces were built. Examples containing curve block cutting, discrete fracture networks (DFN) model, soil-rock mixture slopes, complex shaped geometry, etc. have indicated that the software is robust, efficient, and user-friendly. This software can also generate models for the discrete element method (DEM), discontinuous deformation analysis (DDA), etc. Therefore, the MEG3D can be used as a general pre-processing program for 3D-NMM and other block-based numerical methods.