Baer has been with the studio since it was created four years ago, but during her tenure the flops have piled up.
Among the CBS Films projects that have failed to catch fire with audiences are the Harrison Ford medical drama "Extraordinary Measures," the teen romance "Beastly" and the Jennifer Lopez romantic comedy "The Back-Up Plan."
No CBS Films release has grossed north of $40 million domestically. (Although, for the most part, the studio's films have been low-budget, and it has managed to make money on "Faster," "Beastly" and "The Mechanic.")
Baer, a veteran Sony executive, was given a long leash from CBS chief Les Moonves to experiment and try to to launch the studio.
Indeed, only Moonves' rather mysterious commitment to having a film studio has allowed it to survive, since from a business perspective it appears to make little sense.
"We thank Amy for her important role in building CBS Films," Moonves said in a statement. "Going forward, we remain fully committed to the division¹s focus on a targeted slate of smart acquisitions and quality homegrown productions in all genres. CBS Films is small in the overall size and scope of our company, but continues to fit nicely with the Corporation's premium content strategy."
Baer will transition out of the studio through October, then will produce several CBS Films' projects including "Last Vegas," which start shooting this winter.
The rest of the studio's top executives, such as distribution EVP Steven Friedlander and COO Wolfgang Hammer, will remain place.
Instead of landing on a straight replacement for Baer, there will be a team leadership structure at the top made up of current executives.
After being burned at the box office, CBS has concentrated on picking up a series of genre based films such as the Daniel Radcliffe horror film "The Woman in Black" and the Coen Brothers scripted "Gambit." It also has high hopes for its adaptation of Stephen King's "The Stand," a co-production with Warner Brothers.
Prior to joining CBS Films, Baer was executive vice president of production at Columbia Pictures between 1998 to 2007.
Deadline first reported Baer's departure.