Methods and systems for manufacturing a wavefront-guided scleral lens prosthetic device customized for an eye of a patient include obtaining a first scleral lens prosthetic device with a central optic zone configured to vault over the eye's cornea and a peripheral haptic zone configured to align with the eye's sclera, collecting measurements of any offset and/or rotation of the first scleral lens prosthetic device relative to the eye's pupil and of any aberrations, particularly higher-order aberrations, generating a wavefront-guided profile from the measurements, and fabricating a second scleral lens prosthetic device with the profile on a surface of a central optic zone configured to vault over the eye's cornea and a peripheral haptic zone customized to align with the eye's sclera.