3D imaging is essential for the study and analysis of a wide variety of structures in numerous ap-plications. Coherent photonic systems such as Optical Coherence Tomography (OCT) and Light Detection and Ranging (LiDAR) are state of the art approaches, and their current implementation can operate in regimes that range from under a few millimeters to over more than a kilometer. We introduce a general method, which we call Universal Photonics Tomography (UPT), for analyzing coherent tomography systems, in which conventional methods such as OCT and LiDAR may be viewed as special cases. We demonstrate a novel approach based on the use of phase modulation combined with multirate signal processing to collect positional information of objects beyond the Nyquist limits. Depending on the location of the phase modulator in the system, and associated modulation scheme, we can improve the axial resolution or the maximum measurement distance (unambiguous range).