The board of directors is working with executive search firm Spencer Stuart to find permanent replacements. The audit committee also dismissed KPMG LLP as the company's independent auditor and has begun a search for a new auditor.

The moves come after a rough few months for the company. In September, the Office of Federal Housing Enterprise Oversight released a report based on an eight-month investigation concluding that the government-sponsored enterprise had manipulated earnings and engaged in dubious accounting practices.

And in a Form 8-K filing to the Securities and Exchange Commission in October, the company noted that eight lawsuits against it have either been filed or are in the process of being prepared. Holders of the housing mortgage lender's securities are behind the lawsuits, which, for the most part, accuse Fannie Mae of securities violations with regard to recently scrutinized accounting procedures. Raines and Howard were both named in the suits that had been officially filed at that time.