SAN JOSE, Calif. (AP) – The Securities and Exchange Commission filed civil charges Tuesday against two former Apple Inc. 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 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 Macintosh computer maker to underreport its expenses by nearly $40 million, the SEC said.

The first grant, in February 2001, consisted of 4.8 million options to Apple’s executive team. The second, in December 2001, was a grant of 7.5 million options to Apple’s iconic CEO, Steve Jobs.

Mr. Anderson should have noticed Ms. 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.

Apple’s own internal probe cleared Mr. Jobs and any current officers of misconduct but pointed to “serious concerns” about the actions of two unnamed former employees, now widely believed to be Ms. Heinen and Mr. Anderson.

Shares of Apple were up 57 cents, to $94.08, in Tuesday afternoon trading on the Nasdaq Stock Market.