Evaluating bioscaffolds and its interface with tissue and cells are unsatisfactory with conventional histology, imaging modalities and conventional x-ray micro tomography system (microCT). Histology can take up to a few weeks and are prone to artifacts. Electron optics imaging requires extensive sample preparation, while AFMs are confined to surface characterization of a very small sample area. Conventional microCT lacks the contrast to image soft tissue and cartilage and does not have the resolution to detect fine microstructures. In the current work we have used a novel multiscale CT system to develop a rapid technique for non invasive 3D characterization of a variety of biomaterials, tissue engineering scaffolds and their interaction with soft and calcified tissue, often without much sample preparation or contrast agents, and with spatial resolution from a few microns to sub 50 nm. A clinical application involving evaluation of porosity of a PLGA bioscaffold during fabrication and its subsequent implant and bone quality studies in a patient will be discussed. Other examples include imaging 3D distribution of hepatocyte cells on tissue engineered PCL-collagen scaffold; cartilage imaging in murine bones without contrast agents. Finally, the power of non invasive multiscale tomography characterization of complex biological systems from meso to nanoscale resolution will also be illustrated . Comparison of CT results with conventional histology, SEM and MRI will be shown. The novel Multiscale CT comprises a MicroCT and nanoCT module and uses proprietory optics. Unlike conventional microCTs which rely on point projection technique, hence resolution is limited by source spot size and its sample-source distance, the resolution of the novel CT is not dependant on these parameters. With significantly higher contrast than conventional CTs, it is possible to image most biomaterials and soft tissue without contrast agents.