This study compares two non-contact profilometric systems, the LPM-4 and the Keyence LJ-X8020, to evaluate the lateral layer structures of FDM 3D-printed materials. Four specimens were measured—black PLA, white PLA PRO, transparent violet PLA/PHA and orange PET-G—each printed with identical settings to show how material and color affect measurement accuracy. The LPM-4 profilometer yielded high-density numerical datasets that were conducive to the quantitative surface evaluation (Ra, Rz) of the material. The Keyence system, meanwhile, provided high-resolution 2D and 3D visualizations that were instrumental in conducting a qualitative layer diagnostic analysis of the material in question. Both systems showed that optical and material properties affect measurement accuracy. The results show that integrating different profilometric methods improves understanding of 3D-printed surfaces.