Heat treatment is commonly used during device processing in order to achieve specific functionalities of the devices. How a series of heat treatment applies to accomplish this goal can be found in the literature. However, specific properties of the devices after the treatment are more emphasized than the details of the structural modifications in the industrial applications. In this paper, it is intended to illustrate the fundamental changes in the structure due to heat treatment which result in the desired physical properties of the devices. Two study cases, Ag ion-exchanged soda-lime glasses and aluminum doped ZnO (AZO) films, were illustrated. The changes in chemical states, the structural modification during and after heat treatment are explored. By understanding how the metallic Ag formed and accumulated during annealing, an optimum heat treatment to grow the proper size and density of silver quantum dots in the films are possible. Post annealing effect on the AZO films shows that the crystallinity, the peak positions shifts, and grain sizes were changed after annealing. Both illustrated cases indicate thermally induced changes in chemical state, the stress release, and rearrangement of atoms in materials during and after annealing.