The present invention is directed to system for and methods of real time observing, monitoring, and detecting anomalies in programs' behavior at instruction level. The hardware assist design in this invention provides fine grained observability, and controllability. Fine grained observability provides unprecedented opportunity for detecting anomaly. Controllability provides a powerful tool for stopping anomaly, repairing the kernel and restoring the state of processing. The performance improvement over pure software approach is estimated to be many orders of magnitudes. This invention is also effective and efficient in detecting mutating computer viruses, where normal, signature based, virus detection is under performing.