The Securities and Exchange Commission filed civil charges Tuesday against two former Apple Inc. (AAPL) officers over their alleged roles in backdating stock options. The agency immediately announced a settlement with one of them.

Former Chief Financial Officer Fred Anderson has agreed to pay about $3.5 million in fines and penalties to settle the case, the SEC said.

The case against former general counsel Nancy Heinen will proceed. Her attorneys have vowed to fight the charges.

The commission accused Heinen of participating in fraudulent backdating and altering company records to conceal the fraud. The charges were in connection with two large options grants that caused the company to underreport its expenses by nearly $40 million, the SEC said.

The grants in question were a February 2001 grant of 4.8 million options to Apple's executive team and a December 2001 grant of 7.5 million options to Apple CEO Steve Jobs.

Anderson should have noticed Heinen's efforts to backdate the executive team's grant, but he failed to take steps to ensure that Apple's financial statements were correct, the SEC said.