In order to overcome the difficulties with existing methods for sample immobilization in imaging Halobacterium salinarum (H. salinarum) living in a highly salty medium by atomic force microscopy (AFM), a heat-fixation method was, for the first time, used to overcome existing problems in preparing samples for AFM. The effect on the cell morphology of the heat-fixation method was studied by MAC mode AFM, and was compared with the drop-and-dry and the polylysine-adhesion methods. It was found that the heat-fixation method can be successfully used for preparing Gram-negative and Gram-positive bacteria samples for AFM studies. Using this method, high-resolution AFM images of H. salinarum were obtained. Round protrusions on the cell surface and horn-like protrusions only at one pole of H. salinarum were observed.