In this dissertation, the accuracy and reliability of non-linear finite element computations in application to surgical simulation is evaluated. The evaluation is performed through comparison between the experiment and finite element analysis of indentation of soft tissue phantom and human brain phantom. The evaluation is done in terms of the forces acting on the cylindrical Aluminium indenter and deformation of the phantoms due to these forces. The deformation of the phantoms is measured by tracking 3D motions of X-ray opaque markers implanted in the direct neighbourhood under the indenter using a custom-made biplane X-ray image intensifiers (XRII) system. The phantoms are made of Sylgard® 527 gel to simulate the hyperelastic constitutive behaviour of the brain tissue. The phantoms are prepared layer by layer to facilitate the implantation of the X-ray opaque markers. The modelling of soft tissue phantom indentation and human brain phantom indentation is performed using the ABAQUSTM/Standard finite element solver. Realistic geometry model of the human brain phantom obtained from Magnetic Resonance images is used. Specific constitutive properties of the phantom layers determined through uniaxial compression tests are used in the model. The models accurately predict the indentation force-displacement relations and marker displacements in both soft tissue phantom indentation and human brain phantom indentation. Good agreement between the experimental and modelling results verifies the reliability and accuracy of the finite element analysis techniques used in this study and confirms the predictive power of these techniques in application to surgical simulation.