Our goal is to develop a low-cost tool that can be used to create consistent, partial-thickness defects in rabbit and other large animals with minimal surgical training and that can facilitate pre-clinical testing of lamellar and in situ-forming biosynthetic matrix materials for corneal repair. In this study, three modified trephines were designed to create deep corneal wound defects with consistent depth in large animals. The modified trephines incorporated either 3D-printed parts made from photopolymerizable resins, or custom-cut commercially available Teflon sheets. Wound defects were imaged with optical coherence tomography (OCT), and the depth was analyzed based on the OCT images. The results revealed that an inner-stopper guard trephine had the best performance in creating consistent and precise wound defect depth compared to modified vacuum trephine and custom guard vacuum trephine. A 75% ± 10% cut of the cornea was achieved with the inner-stopper guard trephine. The wound defect depth by created by the inner-stopper guard trephine was independent of the corneal thickness or size of the globes. Although the cut depth of the inner-stopper guard trephine differed by the experience-level of its users, the consistency (standard deviation) of the depth was independent of experience. Our studies provided three cost-efficient animal trephines that can create corneal wounds of consistent depth by lab researchers without extensive training in keratectomy.