A method for making a multi-layer blow molded container (10), the multi-layer preform (10') from which the container is blow molded, and the apparatus (53) for making a liner (24) of the preform utilizes thermoforming of a heated sheet (34) of resin. A vacuum is drawn within a vacuum enclosure (54) that is heated between a pair of spaced heaters (52). A first surface of the heated sheet of resin (34) and a male vacuum mold (56) engages the other surface of the heated sheet of resin which has a concave shape to provide the forming in a manner that prevents crystallinity of the lower freestanding base of the multi-layer container that is ultimately blow molded from the preform (10') made with the thermoformed liner (24).