We propose a visual marker embedding method for the pose estimation of a projection surface to correctly map projected images onto the surface. Assuming that the surface is fabricated by a full-color or multi-material three-dimensional (3D) printer, we propose to automatically embed visual markers on the surface with mechanical accuracy. The appearance of the marker is designed such that the marker is detected by infrared cameras even when printed on a non-planar surface while its appearance can be diminished by the projection to be as imperceptible as possible to human observers. The marker placement is optimized using a genetic algorithm to maximize the number of valid viewpoints from which the pose of the object can be estimated correctly using a stereo camera system. We also propose a radiometric compensation technique to quickly diminish the marker appearance. Experimental results confirm that the pose of projection objects are correctly estimated while the appearance of the markers was diminished to an imperceptible level. At the same time, we confirmed the limitations of the current method; only one object can be handled, and pose estimation is not performed at interactive frame rates. Finally, we demonstrate the proposed technique to show that it works successfully for various surface shapes and target textures.