In this paper, we propose a layout estimation method for multi-layered ink by using PSF measurement and machine learning. This estimation can bring various capabilities of color reproduction for the newfangled 3D printer that can apply multi-layered inkjet color. Especially, the control of translucency is useful for the reproduction of skin color that is overpainted flesh color on bloody-red layer. Conventional method of this layer design and color selection depended on the experience of professional designer. However, it is difficult to optimize the color selection and layer design for reproducing complex colors with many layers. Therefore, in this research, we developed an efficiency estimation of color layout for human skin with arbitrary translucency by using machine learning. Our proposed method employs PSF measurement for quantifying the color translucency of overlapped layers. The machine learning was performed by using the correspondence between these measured PSFs and multi-layered printings with 5-layer neural network. The result was evaluated in the CG simulation with the combination of 14 colors and 10 layers. The result shows that our proposed method can derive an appropriate combination which reproduce the appearance close to the target color and translucency.