An adaptive control and self-tuning procedure is developed to mode-lock fiber laser systems using multiple transmission filters. To recognize average cavity birefringence of multi-filter laser configurations, we propose three classification algorithms that are uniform selection of modes, division of main library to sub-libraries and dynamic library selection from main library. A maximum seeking algorithm is constructed to determine optimal (maximal) waveplate(s) and polarizer(s) setting and, the adaptive control and self-tuning scheme is designed as a combination of maximum seeking and dynamic library selection algorithms. Numerical implementations  show that the proposed self-tuning  scheme achieves to keep multi-filter laser systems mode-locked with high pulse energies circumventing the multi-pulsing instability.