Born in Talcahuano in 1944. He studied Veterinary Medicine at the Austral University. He arrived in Santiago in the 60's where he studied Theater at the Pontificia Universidad Católica de Chile, and then Film at the Escuela de Artes de la Comunicación of the same University. In 1969, he interrupted his studies to work with Guillermo Cahn in the production company Tercer Mundo. There he made his first audiovisual works. He is scriptwriter in "Casa o Mierda" (1969), directed by Guillermo Cahn and Samuel Carvajal in photography. His first documentary as director is "Nütuayin Mapu" (1969).

In 1970 he is hired by the Experimental Film Department. His first work was the production of the short film "No nos trancarán el paso" (1971), by Guillermo Cahn. Later he directed the first feature-length documentary produced entirely by the Film Department of the University of Chile, "Descomedidos y Chascones", which was not released on the planned date due to the military coup.

During the dictatorship, Carlos Flores decided to stay in Chile and dedicated himself to advertising. In 1976, together with Guillermo Cahn, they became partners in the production company Foco Film, dedicated to advertising and documentaries. "Pepe Donoso" was his first documentary after the military coup, a visual document about the life of José Donoso, produced by Guillermo Cahn. For this film, he won the 1977 CINE UC Award and the 1977 Chilean Art Critics Circle Award.

In 1979 he participated in the collective and clandestine production of the documentary short film "Recado de Chile", co-produced by Guillermo Cahn and the ICAIC of Cuba, about the activities that the Agrupación de Detenidos Desaparecidos carried out on Chilean soil. The work was never shown in Chile and was premiered in 1979 at the Lille International Short Film and Documentary Festival (it participated as the work of an "Anonymous Collective"). It was also presented at the First International Festival of New Cinema of Havana 1979; in both instances it won awards. At the end of the decade, Flores began the making of "The Chilean Charles Bronson" (1982). The film, produced by Guillermo Cahn, was recently screened at the 12th Buenos Aires Independent Film Festival BAFICI.

His academic training includes Literature at the Department of Humanistic Studies at the University of Chile, a Diploma in Cultural Criticism at the Arcis University and a degree in Theory and History of Art at the University of Chile. He is a graduate in Theory and History of Art at the same university, whose thesis work was transformed into the book "Eccentrics and Cunning" (2007). In addition to his work at the Chilean Film School, he was Director of the Bachelor's Degree in Documentary Film at the Academy of Christian Humanism. In 2007 he made his last work to date, a co-direction with Miguel Angel Vidaurre called "Corazón Secreto", produced under the auspices of the Chilean Film School.

In 2010 he left the Film School of Chile to join the Film and Television Career at the University of Chile, as Career Director.