Advances in information technology based applications in medicine and biology help to improve the conventional methods of delivering health services by enhancing and complementing traditional approaches of medical education, diagnostic techniques, intra-operative assistance, and pre/post operative services etc. Individualized medical training by virtual simulations and the use of advanced visualization techniques in cell biology will impact the way medicine is practiced and biological processes are understood. Although enhancing visualization and presenting the unreality in a form of blended virtuality is exceedingly accepted in medicine and biology, it brings many challenging but intriguing and intertwined multi disciplinary problems that are required to be addressed. This dissertation addresses the challenges of facilitating the virtual environment systems particularly in the augmented reality and the virtual reality settings that deal with algorithmic problems originated from integration of different components particularly related to surgical simulations. More specifically, the works will be presented here include light microscopic image enhancement (MIBIC algorithm) and its improvement for real-time processing, testing human perception metrics in immersive environments, rasping procedure design and analysis for artificial disc replacement surgery, registration problem in augmented reality system, real-time soft-tissue deformation in virtual reality with a commodity graphical processing unit (GPU), and collision detections for deformable bodies with using hardware assisted spanner (or balls hierarchy).