Nowadays, scientists lay greater emphasis on bio-prospecting of new materials from biological resources. We isolated biogenic micro-silica phytolith from husk of red sorghum with rigid morphologies, to develop bio-compatible scaffolds for use in 3D cultures. Spherical, dumbbell, and saddle-shaped silica phytoliths were extracted by a calcination processes and silica phytoliths with different morphologies were isolated by density gradient centrifugation. The XRD patterns confirmed that silica phytoliths were amorphous. The microscopic images suggested the presence of spherical, saddle, and dumbbell-shaped silica bodies with dimensions of 10-300 mu m. The functional integrity of each spherical-, saddle-, and dumbbell-shaped three-dimensional (3D) silica phytoliths was analyzed on human mesenchymal stem cells. Our results outlined that various forms of silica phytoliths in the form of 3D scaffolds can be used in 3D cell culture models for tissue engineering applications. The results highlighted that these agricultural wastes containing silica phytoliths could be exploited for tissue engineering applications.