Nanosilicate-polysaccharide composite hydrogels are a well-studied class of materials in regenerative medicine that combine good 3D printability, staining, and biological properties, making them an excellent candidate material for complex bone scaffolds. The aim of this study was to develop a hydrogel suitable for 3D printing that has biological and radiological properties similar to those of the natural bone and to develop protocols for their histological and radiological analysis. We synthesized a hydrogel based on alginate, methylcellulose, and laponite, then 3D printed it into a series of complex bioscaffolds. The scaffolds were scanned with CT and CBCT scanners and exported as DICOM datasets, then cut into histological slides and stained using standard histological protocols. From the DICOM datasets, the average value of the voxels in Hounsfield Units (HU) was calculated and compared with natural trabecular bone. In the histological sections, we tested the effect of standard histological stains on the hydrogel matrix in the context of future cytological and histological analysis. The results confirmed that an alginate/methylcellulose/laponite-based composite hydrogel can be used for 3D printing of complex high fidelity three-dimensional scaffolds. This opens an avenue for the development of dynamic biological physical phantoms for bone tissue engineering and the development of new CT-based imaging algorithms for the needs of radiology and radiation therapy.