Presented is a method for making a flexible container. The method implements an injection mold having a collapsible core that expands/moves to define the apertures and, in some embodiments, holds a flexible film in place during the injection mold process and collapses/moves back post-injection molding to allow for the flexible container to be readily removed from the die. In addition, the method described includes a post-injection molding anneal process that is implemented to allow the flexible film to shrink so as to provide for the form-fitting of the film to the molded portion of the container.