As we move forward, and computer technology improves, we will have the ability to utilize programs to look for "red flags" or anomalies within a companies books. The other side of this coin is that this technology can also be utilized to conduct fraudulent operations, and an article in Accounting today even suggests that this will be the direction that fraud goes in 2015.
If a company is suspected of fraud, or a whistleblower comes to the SEC with information fraud examiners will get to work! HOW an auditor investigate it.