The US Securities and Exchange Commission yesterday simultaneously charged and settled with Fred Anderson, who served as Apple’s CFO for eight years and on its board until last October, over claims of improper accounting in 2001.

Anderson agreed to pay $3.5m in ill-gotten gains penalties relating to his windfall from the backdated options, but did not admit or deny any guilt.

He later issued a statement through his lawyer, in which he claimed that he had been assured by Jobs that the stock options in question were being handled properly.

Former Apple general counsel Nancy Heinen has also been charged with stock fraud. The SEC claims she fabricated board minutes in order to back-date options granted to Apple’s executive team in 2001.

All three executives, and three others, benefited from the alleged fraud. The SEC claims that Apple under-reported its expenses by $40m due to the backdating.

Backdating, as the name suggests, is the process of attaching earlier dates to option grants, so executives can benefit from being able to buy shares at historically lower prices, then sell them at the higher later price.

The difference has to be reported as an expense on quarterly earnings statements, which drags on reported GAAP profits. When it discovers companies have not been reporting these charges, the SEC investigates.

In the case of Apple, the SEC alleges improper backdating happened twice in 2001. Once to grant six members of the executive team each a windfall, the second to put millions into Jobs’ pocket.

In the case of the executive team grant, the SEC says that Apple backdated the options from February 2001 to January 17, when the price was lower. The SEC says that Heinen faked documents to show an earlier board approval that never happened, and that Anderson should have known about it.

Anderson, through his lawyer, said he had thought everything was above board, and that Jobs had told him that the Board had given its prior approval and the Board would verify it.

Fred relied on these statements by Mr Jobs and from them concluded the grant was being properly handled, his lawyer’s statement reads.

The Jobs grant was made in December 2001 but backdated to October 2001. The SEC says this was Heinen’s work, and that Jobs walked away with $20m of unexpensed compensation as a result.

The SEC has said it will not go after Apple the company, but reportedly that it has not closed the book on investigating individuals. Other law enforcement agencies are also looking into the case.

Jobs has previously admitted knowing about the options backdating, and apologized to shareholders, but laid the blame with two individuals we now know to be Anderson and Heinen.

The company said it would restate earnings for affected periods last October.