Many quantum systems are being investigated in the hope of building a large-scale quantum computer. All of these systems suffer from decoherence, resulting in errors during the execution of quantum gates. Quantum error correction enables reliable quantum computation given unreliable hardware. Unoptimized topological quantum error correction (TQEC), while still effective, performs very suboptimally, especially at low error rates. Hand optimizing the classical processing associated with a TQEC scheme for a specific system to achieve better error tolerance can be extremely laborious. We describe a tool Autotune capable of performing this optimization automatically, and give two highly distinct examples of its use and extreme outperformance of unoptimized TQEC. Autotune is designed to facilitate the precise study of real hardware running TQEC with every quantum gate having a realistic, physics-based error model.