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Tissue-mimicking phantoms with well-defined properties can help in identifying the potential weaknesses in medical imaging systems. Among the imaging systems, magnetic resonance elastography is a new noninvasive technique used to quantify the shear modulus of biological tissues, and therefore has shown promise in studying liver and brain pathologies. Polyvinyl alcohol (PVA) cryogel prepared by the freeze-thaw technique is a potential candidate for mimicking the mechanical properties of soft tissues and has been extensively used as a phantom material. However, large PVA cryogels suffer from variations in properties, partly due to the low thermal conductivity of PVA solution. The loss of homogeneity in cryogel phantoms is also attributed to inhomogeneous thawing rates during the freeze-thaw cycle. We have used a modified freeze-thaw process that imposes multiple isotherms so as to enhance the homogeneity of the produced cryogels. In addition, we have developed a finite-element modeling tool (a virtual controller) to optimize the temperature profile during the freeze-thaw cycle. Our experimental validations demonstrated the potential of the virtual controller in predicting the optimal temperature profile for the freeze-thaw process (phantom diameters: 60 and 100 mm). A robust simulation framework can fill the gap in the scientific literature with regard to phantom design for medical imaging and will help to reduce phantom development time and cost.