Halladay had surgery last week on his labrum and rotator cuff. He also had an inflamed bursa removed.
Halladay can begin a throwing program in six to eight weeks if everything goes right during rehab.
Halladay, 36, went on the disabled list after experiencing shoulder soreness in April. He was 2-4 with an 8.65 ERA and 35 strikeouts this season.
The two-time Cy Young Award winner is in the final year of his contract with the team and won't fully meet option incentives that guaranteed him $20 million next season if he pitched 225 innings in 2013, and a combined 415 for the 2012-2013 seasons.
Phillies general manager Ruben Amaro Jr. said Halladay feels like he has pretty good range of motion.
"I talked to him [Tuesday]," Amaro said. "He's pretty positive."