The 34-year-old actress split from her director husband, 42, last year following revelations that he had cheated on her with Kirsten Stewart, 22.
Liberty filed the papers at the Los Angeles County Superior Court, asking for spousal support and joint custody of their children Sykla, seven, and Tennyson, five.
In response, Rupert has asked for joint custody and requested that he and Liberty split the court costs between them.
Following the highly publicised affair between Kristen Stewart and Rupert Saunders, Liberty initially kicked him out of their house, later attempting to rebuild their marriage through couples therapy.
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A source close to the couple at the time said: "It was Rupert's suggestion that he go to therapy with Liberty.
"He will do anything to save his marriage because he loves his wife and knows he screwed up.
"They have been married since 2003, and have two children together, they have a life together.
"Rupert is willing to do absolutely anything and everything he can to save his marriage, he knows this is the worst mistake of his life, and he cannot believe he was so stupid.
"The thought of losing his wife and children, who he loves more than anything in the world is killing him."
Kristen Stewart initially split from her long term boyfriend Robert Pattinson following the affair last year.
However the two managed to put the scandal behind them, rekindling their relationship before embarking on a worldwide promotion of the final Twilight film ‘Breaking Dawn Part Two’.