Study of the microstructure of electronic materials can be enhanced by using high resolution transmission electron microscopy (TEM) combined with the technique of digitized image analysis. We show here a practical image analysis method for the microstructures of acceptor graphite intercalation compounds (GICs) with CuCl2 and FeCl3 intercalates. The two dimensional fast Fourier transform (2D-FFT) was used for the frequency analysis of the TEM pictures. It is found that the lattice images of CuCl2-GICs consist of different frequency images corresponding to specific frequencies. The detailed features of the stage-1 structure of the FeCl3-GICs is extracted quantitatively by this method from a relatively indistinct TEM picture. The stage structure of the CuCl2- and FeCl3-GICs are further investigated by analyzing the reconstruction of the TEM images by means of the two dimensional inverse FFT (2D-IFFT).