Abstract-Bacteria exist in a variety of groups of shapes, sizes, and single or multiple cell formations. In this paper, the level set shape reconstruction technique, the method of moments, and the marching cubes methods are integrated in the high frequency band for imaging three dimensional bacteria. The time step and the resolution of the marching cubes method are investigated to smooth the error function of the level set and hence speed up the convergence at high frequencies. The numerical results demonstrate the robustness of the level set algorithm for the detection of bacteria based on their shapes. The three dimensional shape reconstructions of unknown bacteria can be utilized to classify biological warfare agents.