Medical simulation tools have a potential of revolutionizing the practice of medicine by assisting clinicians in carrying out difficult medical procedures. For example, Simulation tools capable of predicting tissue mechanical response can provide clinical therapy learning environment via virtual reality. While such tools improve training proficiency, they enhance patient safety and cost less compared to conventional training on real patients. Intraoperative image based clinical procedures where images are updated to account for tissue deformation during medical procedures is another area where such simulation tools play a very significant role. Brachytherpay of the prostate, breast or lung are examples where these tools can be used effectively to update preoperative high quality images for the purpose of accurate placing brachytherapy seeds. While Finite Element (FE) Analysis is known as an accurate method in finding soft tissue deformation, it is not fast enough in applications where real-time simulation of tissue mechanical response is needed. In this presentation, a novel technique based on FE analysis will be introduced for estimating soft tissue deformation. This technique has proven to be not only accurate, but also very fast. The technique can be applied for real-time or near real-time soft tissue deformation calculation irrespective of the complexities arising from the tissue constitutive law or loading. To calculate the deformed shape of an organ, the technique involves a preprocessing step in which FE analysis is performed on a model class of corresponding organ obtained from a large number of subjects, followed by statistical analysis. Given the high degree of similarity between the shapes of each specific organ in different subjects or between shapes of a patient’s organ over time, this technique is ideal for applications where real-time or near real-time estimation of a specific organ deformation is desired. To validate this technique and demonstrate its capabilities in clinical procedures, a number of biomedical applications will be shown including prostate elastography.