Objective: To conduct a standardized method for cavity preparation on the palatal surface of rat maxillary molars and to introduce a standardized method for tooth correct alignment within the specimen during the wax embedding procedure to better detect cavity position within the examined slides. Materials and methods: Six male Wistar rats, aged 4-6 weeks, were used. The maxillary molars of three animals were sectioned in the frontal plane to identify the thickness of hard tissue on the palatal surface of the first molar which was (250-300µm). The end-cutting bur (with a cutting head diameter of 0.2mm) was suitable for preparing a dentinal cavity (70-80µm) depth. Cavity preparation was then performed using the same bur on the tooth surface in the other three animals. Rats are then euthanized before dissecting, fixing, and demineralizing the teeth. For better alignment of teeth samples during the waxing procedure, K-file endodontic instrument size #8 was dipped in Indian ink. The file tip was inserted on the jaw bone at the buccal side of the tooth in a region opposed to the prepared cavity on the palatal side. Moreover, a small Dycal applicator instrument was used to mark the jaw bone on the mesial side of teeth samples as an orientation for the cutting surface. Results: Well-defined sections were obtained with a clear cavity extension within dentin and without any signs of pulp exposure in all samples. Conclusion: This pilot was conducted to perform an easy procedure for cavity preparation in rat molar teeth to obtain a clear histopathological section.