Atomic force microscopy images of the surface coatings of bacterial spores can be analyzed by wavelet analysis to rapidly determine the characteristic morphology of the spore coat The identification of bacterial spores in the environment is an important problem for preventing disease, identifying bacterial contamination of air, water, and soil, and evaluating the effects of chemicals on bacteria. In this work, we analyze AFM data of the native surface topography and ultra structure of spore coats of native Bacillus atrophaeus and Bacillus thuringiensis. We show that if the analysis of the images is done as a function of the rotation angle of the image observation, the morphology and the characteristic sizes of the bacterial coats can be accurately analyzed. The technique has potential to rapidly identify bacterial spores and viruses if a library of images of various bacteria are obtained.