The development of imaging technologies such as computed tomography and magnetic resonance imaging has made it easier to obtain three-dimensional data of the internal human body. Visualizing these data helps us to understand the complicated internal structure of the human body. Transparent stereoscopic visualization using depth information is a good way to visualize internal body structure. However, the position and depth information often become unclear when three-dimensional data are rendered transparently. In this study, we aimed to understand the structural understanding and correct depth perception in transparent stereoscopic visualization, and examined how depth perception changes by overlaying multiple iso-surfaces on transparently rendered image. The experimental results showed that multiple iso-surfaces improved the accuracy of perceived depth. It was effective when the opacity of the inner iso-surface was high and the distance between the inner iso-surface and the outer iso-surface was large.