A system and method is provided for restoring a 3D tomographic model of the Earth's subsurface geology from the present-day to a past restoration time. Whereas at the present time all faults represent active discontinuities, at a past restoration time some faults have not yet formed. Accordingly, the restored model divides the fault network into τ-active faults (discontinuous surfaces for faults that intersect the layer deposited at the past restoration time) and τ-inactive faults (continuous surfaces for faults that do not intersect the layer deposited at the past restoration time). A new 3D restoration transformation is also provided that uses linear geological constraints to process the restoration model in less time and generate more accurate geological images.