A semiconductor manufacturing apparatus includes a first program on a controller and a second program on an interface board between the controller and controlled devices. Both of the programs update their own counters and exchange their counter values with each other, serving as bi-directional software watchdog timers (WDT). If a counter value of the first program on the controller sent to the second program on the interface board is determined to be abnormal by the second program, the second program on the interface board sends commands to the controlled devices to terminate output so that the apparatus is navigated to a safe mode. The first program similarly monitors the counter values of the second program for anomalies. This bi-directional software WDT can be implemented as add-on to software programs that already exist in the controller and the interface board, therefore, this implementation does not incur extra cost of hardware of the apparatus.