Tyndall National Institute has extensive experience in 2D and 3D modelling of light interaction with diffuse media using powerful tools such as MATLAB and NIRFAST. These tools can be combined with clinical CT scans of biological structures and organs to generate a light interaction models with complex, multi-layered geometries. Detailed models of light transmission through biological tissue are an essential source of supporting information when designing and building systems aimed at deep tissue optics. These models can be used to inform the illumination and detection strategies that need to be employed by measurement systems to achieve an optimal SNR.