In this article, the numerical and experimental free vibration analyses of PLA-based composite plates with different filling geometries were carried out. Firstly, the natural frequencies and modal shapes were obtained from finite element (FE) methods to characterize the vibration behavior of the plates. The obtained results were compared with experimental testing of the three-dimensional (3D) produced plates. In the comparison, it was seen that the finite element analysis and the experimental results were quite close to each other. It was also observed that the highest frequencies are measured by a triangle, then the grid and honeycomb. Moreover, higher frequencies and lower weights are possible with the triangle pattern fill. On the other hand, it is noted that the types of filling structures do not affect the modal shapes of the 3D plates. Thus, the results of this paper are of utmost importance for getting light structure and high frequencies.