Early detection and diagnosis of skin cancer is essential to treating the malignancy and preventing death. Subsurface features and depth information are critical in evaluating a skin lesion for this early malignancy screening. We present a novel voxel-based Monte Carlo simulation of light propagation in skin tissue which runs in a highly parallel environment on desktop graphics processors, resulting in an extremely fast simulation of millions of photons in less than one second. We then use this model in a genetic algorithm for the inverse 3D volume reconstruction of a skin lesion, given a set of multispectral images obtained using non-invasive transillumination imaging. Our method demonstrates improved accuracy at a superior resolution to existing methods.