Production will resume in the spring on 12 episodes slated for a late 2009 premiere, said Robert Greenblatt, Showtime's president of entertainment.
Duchovny, who is also one of the executive producers of the series, won a Golden Globe Award for his role as a self-destructive novelist/blogger with weaknesses for sex, drugs and rock 'n roll.
Natascha McElhone and Evan Handler co-star in the show, which centers around the unique and sophisticated world of the hedonistic Hank Moody, who struggles to raise his Goth-loving teenage daughter while still carrying a torch for his disapproving ex-girlfriend.
"This unapologetic show, about a group of characters led by the inimitable David Duchovny, has quickly established itself as one of our signature comedy series," Greenblatt said. "Beneath its veneer of debauchery, however, is a complex take on love and adult relationships that surprisingly turns poetic and romantic just when you least expect it."