The control and prediction of morphological changes in annealed void microstructures is an essential and powerful tool for different semiconductor applications, for example, as part of the production of pressure sensors, resonators, or other silicon structures. In this work, with a focus on the void shape evolution of silicon, a novel simulation approach based on the level-set method is introduced to predict the continuous transformation of initial etched nano/micro-sized cylindrical structures at different annealing conditions. The developed model, which is based on a surface diffusion formulation and built in COMSOL Multiphysics^® (Stockholm, Sweden), is introduced and compared to experimental literature data as well as with other analytical approaches. Some advantages of the presented model include the capability of simulating other materials under similar phenomena, the simulation of any possible initial geometry, and the visualization of intermediate steps during the annealing processing.