Using atomic force microscope (AFM), we investigated the images of Pars influenza virus (PIV) under different treatment conditions and observed the different appearances of the virus and its ultra-microstructure from the exterior to the interior. From the 2D images under transmission electron microscope (TEM), we could see that the surfaces of PIV particles exhibited spherical and band-shaped 'tufts'; from the 3D images under AFM, we could further observe the whole spherical virus particles and their detailed surfaces, which exhibited round and band-shaped 'tufts'. Comparing the images under TEM with those under AFM, we found that the latter could reveal the surface topograph and ultramicrostructure of viruses more truly than did the former. The samples of viruses were treated by Tritonx-100, the lipid envelopes of virions were partly or completely resolved, and then most of their capsids were exposed. We could observe the different appearances of the virions under AFM, the lipid envelopes of which were gradually removed. The samples of viruses were also treated by SDS, and the RNA was released from the virions. From the AFM images, we could see the structure of the RNA. It was thus clear that AFM could be used to investigate the different appearances and ultramicrostructure of viruses rapidly and efficiently.