Kinesthetic appreciation of anatomy models serves to activate a concrete sensory experience that enhances 3D visuospatial mental mapping of anatomical structures. However, most commercially available plastic anatomy models are costly and do not provide tactile sensation similar to the organ or structures. Polymeric materials have been used widely in additive manufacturing to produce human brain models, however, none of the models resembles accurate feeling. The aim of this study is to produce 3D printed anatomical models using customized soft 3D printing filament from thermoplastic Polyurethane (TPU) and two types of rubber, which are ethylene propylene diene monomer (EPDM) and styrene butadiene rubber (SBR) compounds. Actual human brain MRI scans are used to form 3D-printed anatomy models. The MRI image obtained was in DICOM format, exported into 3D slicer software for specific brain parts extraction (whole brain, brain ventricles, circle of Willis, and dural venous sinuses), and converted into STL format for 3D printing. For material processing, the blending of TPU/EPDM and TPU/SBR were successfully fabricated using an internal mixer (Haake) and extruded into filament using a single screw extruder with the aid of a filament winder. The human brain model was then printed using 3D Printer (Ender 3). It was found that all TPU blends were able to be printed into brain anatomy models but the properties of the materials were greatly affected by rubber types and compositions of the added fillers. The addition of more than 30% of the fillers gave difficulties in processing, probably due to inconsistent viscosity that led to phase separation.