After the 2003–04 season, Modrý left the Kings as an unrestricted free agent and signed with the Atlanta Thrashers. He returned to the Czech Extraliga and played for HC Liberec during the 2004–05 NHL lockout. After only one season with Atlanta, Modrý was traded along with Patrik Štefan to the Dallas Stars for Niko Kapanen and a 2006 7th round draft pick. After playing half of the 2006–07 season with the Stars, Dallas sent him back to the Kings as part of a deadline-day deal to acquire former Kings teammate Mattias Norström. A year later during the following season, Modrý was on the move again as the Kings traded him to the Philadelphia Flyers for a 2008 3rd round draft pick.