Lee, a former deputy general counsel and head of patents and patent strategy at Google, had been the acting director of the office. She started with the agency in 2012 as the first director of the patent office's Silicon Valley outpost.
The agency has been a focus of congressional efforts at patent reform aimed at curbing patent litigation in federal court.
The patent office has been criticized for approving what some say are weak software related-patents that have formed the bulk of the litigation.
Robert Stoll, a 29-year veteran of the agency and its commissioner of patents from 2009 to 2011, said Lee's main task will be to improve the quality of patents granted by the agency.
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"Assuring better quality patents will help blunt the patent troll problem," said Stoll, now a partner at the law firm of Drinker Biddle & Reath in Washington, D.C., using a term some use for companies that profit from patent lawsuits instead of making products.
Another complaint has been the agency's long backlog in examining patents. In December 2011, the unexamined backlog was almost 722,000 patents. It currently stands at 602,265, according to the agency's website.
The Senate on Monday also approved Daniel Marti to be the White House's intellectual property enforcement coordinator, otherwise known as the "IP Czar."