1. A fault detection and isolation system for detecting and isolating faults in a helicopter comprising: an interface coupled to at least one helicopter subsystem and a processor, wherein said interface is a stand-alone module and comprises means for transferring data between the helicopter subsystem and a processor, and wherein the interface comprises a character conversion module comprising means for converting characters transferred between the helicopter subsystem and a processor, a data conversion module comprising means for converting data transferred between the helicopter subsystem and a processor and a format conversion module comprising means for converting a format of data transferred between the helicopter subsystem and a processor; a processor coupled to the interface, comprising a memory including software instructions for a test program sequence adapted to cause the processor to perform the steps of: identifying at least one subsystem of the complex system for testing; generating a test sequence defining an order of testing of the subsystems identified for testing and an order of individual tests to be performed on each subsystem identified for testing; skipping subsystem tests from a previous test program sequence that have been successfully completed within a predetermined period of time prior to beginning another test program sequence, wherein skipping is performed when a variable is a first state; generating periodic built-in-test commands; generating interface test commands; generating initiated built-in-test commands; generating manual test prompts receiving test result data from a periodic built-in-test, an interface test, an initiated built-in-test and a manual test; processing the test result data, wherein processing test results data comprises conversion of built-in-test codes from numeric values into text messages; detecting and isolating any faults to one or more candidate components associated with the detected faults; and storing the results in a database, wherein the processor detects and isolates faults in the helicopter.