A psychophysical experiment using 3D printed samples was conducted to investigate the change of perceived color differences caused by two different illuminations and two 3D sample shapes. 150 pairs of 3D printed samples around five CIE color centers [Color Res. Appl. 20, 399-403, 1995], consisting of 75 pairs of spherical samples and 75 pairs of flat samples, with a wide range of color differences covering from small to large magnitude, were printed by an Mcor Iris paper-based 3D color printer. Each pair was assessed twice by a panel of 10 observers using a gray-scale psychophysical method in a spectral tunable LED viewing cabinet with two types of light sources: diffuse lighting with and without an additional overhead spotlight. The experimental results confirmed that the lighting conditions had more effect on the perceived color difference between complex 3D shapes than between 2D objects. The results for 3D and 2D objects were more similar under only diffuse lighting. Current 3D results had good correlations with previous ones [Color Res. Appl. 24, 356-368, 1999; J. Opt. Soc. Am. A 36, 789-799, 2019] using 2D samples with large color differences, meaning that color-difference magnitude had more effect on perceived color differences than sample shape and lighting. Considering ten modern color-difference formulas, the best predictions of the current experimental data were found for CAM02-LCD formula [Color Res. Appl. 31, 320-330, 2006]. For current results, it was also found that predictions of current color-difference formulas were below average inter-observer variability, and remarkable improvements were found by adding power corrections [Opt. Express 23, 597-610, 2015].