Recently introduced ultrasonic instrumentation techniques for root end preparation have revolutionized the field of endodontic surgery. The specially designed tips offer improved access to the root end and create more conservative root and preparations while decreasing the amount of retained debris. This study compared the cleanliness of root end preparations made using ultrasonic instrumentation with that of those prepared in a traditional manner using a microhandpiece bur. We used 10 extracted maxillary human premolars and molars. After cleaning, shaping, and obturation of the root canals, a 3 mm root end resection perpendicular to the long axis of the root was performed with a carbide fissure bur. The roots were randomly divided into two groups and root end preparations were made using the two aforementioned techniques. The roots were longitudinally split and sputter-coated with gold for scanning electron microscopic study. Three independent dentists used a standardized grading system to evaluate the cleanliness of the root end preparations. The ultrasonic preparation had significantly less superficial debris and a thinner smear layer than the microhandpiece preparation (p < 0.05). There were no significant differences between the canal and isthmus portions of the root end preparations within each group in either superficial debris or smear layer. This indicates that cleaner surfaces for root end cavities are created using ultrasonic retrotips than using microhandpiece burs.