Zambrano, 25, who also was eligible for third-party assistance last year but settled on a one-year, $6.5 million contract, was one of three Cubs who filed on Friday, joining Mark Prior and Will Ohman.
"I'm sure we'll be sitting down with Carlos' representative at or right before Spring Training," Cubs general manager Jim Hendry told the Chicago Tribune. "We've always been fair to the guys we'd like to keep, as our past would indicate."
The Cubs have avoided every salary arbitration hearing since 1993, and most recently they re-signed first baseman Derrek Lee (five years, $65 million last April), Kerry Wood (three years, $32.5 million in January 2004) and Aramis Ramirez (five years, $75 million in November) before they became free agents.
Zambrano, who has a 46-21 record and 3.14 ERA in the past three seasons, would be eligible for free agency after the 2007 season.
The number of filings this year is slightly higher than in 2006, when 94 players filed. However, just 43 of them exchanged salary figures, and six went through a hearing.
The Oakland Athletics, who have had more players (34) go through a hearing than any other Major League organization during the history of salary arbitration, had seven players file on Friday, tying the Pittsburgh Pirates for the most this year.
Morneau, who made $385,000 last season, Minnesota Twins teammate and AL batting champion Joe Mauer ($400,000), along with National League hitting champ Freddy Sanchez of the Pittsburgh Pirates ($342,000), also were on the list of 106 players that filed.
Florida Marlins pitcher Dontrelle Willis ($4.35 million last season), Houston Astros reliever Brad Lidge ($3.975 million) and third baseman Morgan Ensberg ($3.8 million), Los Angeles Angels closer Francisco Rodriguez ($3.775 million), Prior ($3.65 million), Philadelphia Phillies center fielder Aaron Rowand ($3.35 million) and Arizona Diamondbacks pitcher Doug Davis ($3.2 million) also filed on Friday.
The San Francisco Giants were the only organization that didn't have any players eligible for salary arbitration, while the World Series champion St. Louis Cardinals had one, outfielder So Taguchi, as did the Chicago White Sox, third baseman Joe Crede.