Second harmonic generation (SHG) is a well-established optical modality widely used in biomedical optics to image collagen based tissues. The coherent signal of the forward direction SHG produces a high resolution image that can resolve individual fibers (groups of fibrils). In highly ordered collagen lamellae, such as in the corneal stroma, it is important to determine the orientation of the fibers as they contribute significantly to the biomechanics of the tissue. However, due to the crimped structure of the fibers, it is challenging to robustly determine their orientation using an independent computational method, compared to the straight fibers problem. Previous work in the field used the polarization of the fundamental or other techniques involving a more manual selection of the orientation, in order to differentiate between various directions in corneal structures. Yet those lack accuracy and independency. We present a robust independent technique to determine the orientation of the fibers in the corneal structure. The experimental results presented here, taken from different lamellae, demonstrate strongly the correct orientation.