Techniques for improved diagnosis, treatment, and monitoring of corneal pathologies use enhanced mapping of the cornea or corneal regions, to develop three-dimensional mapping of corneal thickness, while retaining particular corneal micro-layer thickness data. Anterior and posterior surface identifications, along with surface apex determinations, are used for registration of segmentation of these micro-layers. 3D heat maps and bull's-eye maps are generated from resulting thickness date. The maps provided enhanced evaluation and diagnosis of a corneal pathologies, such as keratoconus, pellucid marginal degeneration, post-refractive surgery ectasia, keratoglobus, corneal transplant rejection and corneal transplant failed grafts, Fuchs dystrophy, corneal limbal stem cell deficiency, dry eye syndrome, and post-corneal collagen crosslinking evaluation.