Embodiments of systems and methods for substrate thermal processing using a hot plate with a programmable array of lift devices for multi-bake process optimization are presented. In an embodiment, an apparatus includes a base with an upper surface configured to receive the substrate. The base may include at least one heater for heating the substrate while on or in the vicinity of the base, and a plurality of lift devices configured to selectively extend from the upper surface of the base to support the substrate above the base when extended, and allow the substrate to rest on the upper surface of the base when retracted, each lift device being actuated independently of the other lift devices by an actuating mechanism. Additionally, the apparatus may include a controller for controlling the plurality of actuating mechanisms.