Since germanium has a high extinction coefficient in the near infrared (NIR) region compared to silicon, germanium membranes with their thickness controlled are used as a NIR photodetector with the ability to absorb a specific wavelength. In addition, germanium membranes with an underlying cavity become Fabry-Perot resonators that can selectively pass light of a specific wavelength associated with the height of the cavity. To advance aforementioned optical applications of germanium membranes and cavities, it is crucial to control the membrane thickness and the cavity height with high precision. In this paper, germanium-on-nothing structures were fabricated by high-temperature vacuum annealing near the melting temperature to accelerate the self-assembly. By controlling the profile of the initial microscale hole arrays with aspect ratio more than 10, thick single and double membrane structures with microscale thickness were fabricated, and a method to predicting the required annealing time at a given temperature was proposed. In addition, a method that can prevent defects on the germanium surface during high-temperature vacuum annealing was proposed.