Accurate color reproduction is an essential parameter in many 3D printing applications. Although current technologies in full-color 3D printing have enabled the reproduction of thousands of colors, reproducing the precise target color is still challenging and requires tuning. In this paper, we integrate halftoning with a multi-layer printing approach, where ink is deposited at variable depths, to improve the reproduction of tones and fine details in poly-jet 3D printing. The proposed approach is implemented using a manually controlled ink placement add-on for a commercial 3D printer and is compared to the default software of that printer. Results demonstrate that the proposed multi-layer halftoning performs more accurately in reproducing the tones and details of the target appearance.