A modular flight control strategy is presented here to demonstrate the improved command tracking performance with fault tolerance and reconfiguration capabilities. The modular control design process consists of inner and outer loop design concept, where outer baseline controller feedback loop ensures the stability and robustness and inner reconfigurable design is responsible for the fault-tolerance against actuator faults/failures. This guarantees augmented autonomy and intelligence on board aircraft for real time decision and fault tolerant control. Requirements for aerospace cyber physical systems (ACPS) and software are far more stringent than those found in industrial automation systems. The results shows that fault tolerant aspect is mandatory for ACPS, that must support real time behavior and also requires ultra-high reliability as many systems or/sub-systems are safety critical and require certification. © 2014 Springer Science+Business Media Singapore.