Borders has filed for Chapter 11 bankruptcy and plans to close hundreds of stores across the U.S., including several in the Bay Area.

The second largest bookstore chain will close nearly a third of its 642 stores and about 6,000 employees will be laid off.

Borders owes millions of dollars to publishers, who must now decide whether they should continue to do business with a bookseller that has been unable to pay its bills.

The company said it is losing nearly $2 million a day at the stores it plans to close, all of them superstores. According to documents filed with the U.S. Bankruptcy Court in New York, clearance sales could begin as early as this weekend.

Borders will continue to honor its gift cards and loyalty program.