Optical coherence tomography (OCT) has gained momentum on segmenting anterior corneal substructures, such as treatment-induced flaps and lenticule cuts created by femtosecond lasers. However, recent semi-automated methods rely on manual markers, which can introduce bias and variability. In this work, we present an automated algorithm designed to overcome the limitations in the geometric quantification of intrastromal cuts produced by two different femtosecond lasers, using a unique imaging system. Our analysis, conducted on peri-operative segmentations of goat eyes, aims to demonstrate the method’s potential for contributing to ongoing efforts and enhancing clinical outcomes in refractive surgery treatment.