A method of operating a film forming apparatus includes forming a carbon film on each of surfaces of a plurality of objects held by a holding unit in a processing container and performing a cleaning process with a cleaning gas to remove an unnecessary carbon film adhered on a inside of the processing container, wherein the method further includes, before the forming of the carbon film, forming, on a surface of a member contacting a processing space in the processing container, a tolerant pre-coating film which has a tolerance to the cleaning gas and improves adhesion of the carbon film to the surface of the member. Accordingly, the adhesion of the carbon film is improved, and further, the tolerant pre-coating film remains even when the cleaning process of removing the unnecessary carbon film is performed.