Patient specific organ and tissue mimicking phantoms are used routinely to develop and assess new image-guided intervention tools and techniques in laboratory settings, enabling scientists to maintain acceptable anatomical relevance, while avoiding animal studies when the developed technology is still in its infancy. Gelatin phantoms, specifically, offer a cost-effective and readily available alternative to the traditional manufacturing of anatomical phantoms, and also provide the necessary versatility to mimic various stiffness properties specific to various organs or tissues. Here we describe the protocol to develop patient specific anthropomorphic gelatin phantoms of different organs, assess the faithfulness of the developed phantoms against the patient specific CT images, and demonstrate the use of the manufactured phantoms for various biomedical applications. We build the gelatin phantoms by first using additive manufacturing to generate a mold based on patient specific CT images, into which the gelatin is subsequently poured. We evaluate the fidelity of the phantoms against the virtual model generated from the patient specific CT images, as well as against the mold used to manufacture the phantoms. We also demonstrate the use of the manufactured phantoms for biomechanical modeling applications. These techniques enable researchers to mimic and predict pre- to intra-operative organ deformation in vitro, then assess the biomechanical model-based predictions against ground truth data. We used two methods to emulate the sampling of the intra-operative surface landmarks of a liver phantom: the former method entailed the segmentation of the phantom CT image post-deformation, and the latter consisted of scribing the surface of the liver phantom with an optically tracked stylus. The collected data, along with prescribed boundary conditions, were imported into the FEBio, an open-source modeling software, and used to predict the displacement field that best maps the pre-operative liver phantom model extracted from the corresponding CT image pre-deformation to match the deformed, intra-operative liver model. These experiments confirm that the employed protocol provides a reliable, fast, and cost-effective method for manufacturing faithful patient specific organ emulating gelatin phantoms and can be applied or extended to a wide variety of image-guided intervention and broad biomedical applications.