HybGe-Flow3D is a library designed for solving multiscale fluid flow problems in complex, uncertain 3D and 2D geometries. This software is maintained by Numerical Solutions, Inc. The first version of this software was developed under the partial support of the National Science Foundation on the projects NSF DMS-1115827 ”Hybrid modeling in porous media” (PI: M. Peszynska) and NFS DMS-1522734 ”Phase transitions in porous media across multiple scales” (PI: M. Peszynska).