An application is developed for viewing scanning tunneling microscope (STM) data stereoscopically by using alternating-pair glasses and the TV-1024/32 32-bit/pixel graphics accelerator system. Arbitrary viewer position, view, and light source direction are allowed. The steps used for generation of the stereoscopic views are outlined. Due to the large size of the data set (up to 400 X 400 uniform grid) several computational optimizations are used. Symmetry of the data set is used to remove computational redundancies during triangulation and shading processes. Generation of the left eye and right eye view matrices is explained, as well as the transformation of the physical interocular distance of the viewer into the viewing coordinate system. Stereoscopic slides of gold, graphite, and other atomic structures are presented.