Apparatus for filling containers having stoppers that are penetrable for filling the containers with a substance, and thermally resealable for thermally sealing the resulting hole. A container support supports at least one such container in a substantially fixed position during filling and resealing. A manifold drivingly mounted over the container support comprises (1) a cartridge including a filling needle for penetrating the resealable stopper and introducing a substance therethrough into the container, a mount for mounting the cartridge on the manifold, and a removable cover releasably coupled to the mount for covering the filling needle during transportation, installation and/or removal of the cartridge from the manifold. The manifold includes a thermal source for heating a penetrated region of the stopper and, sealing the hole.