Obtaining corneal microlayer thickness maps for different corneal microlayers is important for the diagnosis of different eye diseases such as Fuchs dystrophy, Keratoconus and corneal graft rejection. These diseases are common eye diseases and they affect the vision of millions of people in the united states. Early diagnosis of these diseases can help in treating them and preventing their progression. Optical Coherence Tomography (OCT) is a revolutionary technology that is non-contact and non-invasive, therefore, it is suitable for imaging the eye in vivo. The corneal OCT images contain the different microlayer structures of the cornea. These microlayers appear as hyper-reflective and hypo-reflective structures in the corneal OCT image. In this work, we are able to obtain the corneal microlayer thickness maps using a complete 3D OCT image of the cornea. We detect the corneal microlayers in each 2D OCT image using our proposed segmentation methods. We construct the 3D surfaces of corneal microlayers by mapping the detected microlayers in 2D OCT images into 3D then using interpolation. Finally, the inter-surface distances are corrected using Snell’s law and the thickness maps are generated. We developed our own customized software using Matlab which is capable of performing all the steps to generate the corneal microlayer thickness maps. The data generated by our software is further used for the quantification of different corneal diseases and for comparing them statistically with normative data.