This paper introduces a novel, computationally efficient, and practical atmospheric tomography wavefront control architecture with separate minimum variance laser and natural guide star mode estimation. The architecture is applicable to all laser tomography systems, including multi conjugate adaptive optics (MCAO), laser tomography adaptive optics (LTAO), and multi object adaptive optics (MOAO) systems. Monte Carlo simulation results for the Thirty Meter Telescope (TMT) MCAO system demonstrate its benefit over a previously introduced “ad hoc” split MCAO architecture, calling for further in-depth analysis and simulations over a representative ensemble of natural guide star (NGS) asterisms with optimized loop frame rates and modal gains