To overcome the non-physical limitations to 2D structural restoration tools, efforts are being made toward developing 3D mechanics-based methods, which respect both mass and linear momentum conservations. 3D methods remove many common assumptions in 2D techniques that are often violated in nature, such as line-length and area conservation or constant boundary condition (BC) displacement. However, 3D restorations have challenges of their own that must be overcome to produce accurate, physical representations of rock deformation. One of the greatest challenges is choosing geologically and physically reasonable BCs. These are often based on accepted geometric assumptions, such as flattening and unfolding a datum horizon while simultaneously removing fault offset. However, these BCs, as based on kinematic hypotheses, may lead to unphysical configurations. In addition, non-physical BCs are often required in order to ensure numerical convergence (e.g. fixing degrees of freedom), adding uncertainty to the result. Understanding the forward deformation process is crucial for defining proper BCs and accurate interpretations of a restoration. In this study, we perform a 3D restoration on the structures formed from a 3D analog model. Restoring a forward model provides a priori knowledge of viable BCs to guide our restorations without adding unknown uncertainty to the result. The analog experiment was a 3D forward model of a gravity-driven extensional system with sand layers above a ductile zone, no pre-existing fault architecture and a 1.5° basinward dip. Sedimentary layers were added as growth strata throughout the forward model, recording the timing and kinematics of fault activity and fold growth. The analog model produced two prominent grabens, several half-grabens, salt welds and secondary fault structures. Using BCs defined from knowledge of the undeformed and deformed states, we perform a sequential 3D restoration of this extensional system. These BCs at each time-step are constrained by video capturing the complete forward deformation sequence. These findings are the first to document how accurate BCs add value to 3D restoration techniques. Moreover, restoring the complex structures in our model provides fundamental insight into the temporal evolution of 3D extensional structures, akin to natural suprasalt basins like GOM, Brazil and Angola. This clears the path for increasing accuracy in strain evaluation and assessment of paleo-basin geometry.