Lee is a former deputy general counsel and head of patents and patent strategy at Google, the search engine giant.
Currently head of the U.S. patent office's Silicon Valley outpost, Lee begins her new job on January 13.
The USPTO has been without a director since David Kappos, a former International Business Machines Corp executive, departed on February 1 to return to private practice. Acting director Teresa Stanek Rea has also left the agency.
It was not known when a permanent director would be named for the USPTO, which is part of the U.S. Department of Commerce and awards patents and registers trademarks.
Lee said she planned to attack the backlog of unexamined patents and work to improve patent quality, an issue at the center of the ongoing debate over frivolous infringement lawsuits.
Google has been in the fight against "patent assertion entities" which buy or license patents and sue companies for infringement, but Lee said she would be even-handed in handling disputes.
"None of the policy positions of my former employers has guided my work," she said. "I certainly would be very welcoming of everybody's input."
Lee has an engineering degree from the Massachusetts Institute of Technology and a law degree from Stanford Law School.
One perennial complaint about the patent office has been its backlog.
In December 2011, the unexamined patent backlog was almost 722,000 patents. It was down to 591,665 applications last August, while the most recent number was 590,070, according to the patent office.
Another problem facing the U.S. Patent and Trademark Office is implementing a new inter partes review system required under 2011 patent reform, said Bernard Knight, a former general counsel with the patent office who is now at McDermott Will and Emery.
There have been 697 challenges, and they each must be handled within a year with no additional resources, he said.
"They are meeting it so far, but it's a huge challenge and it's a brand new law. They're like trials," he said.
Former director Kappos had been popular because of his efforts to upgrade the technology for examiners, reduce the backlog of applications in part by adding examiners, and improve the quality of patents that are issued.
© Thomson Reuters 2013