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Manufacturing processes of custom implant abutments may contaminate their surfaces with micro wear deposits and generic pollutants. Such particulate debris, if not removed, might be detrimental and provoke inflammatory reactions in peri-implant tissues. Although regulatory guidelines for adequate cleaning, disinfection, or sterilization exist, there does not appear to be a consistent application and data on the amount and extent of such contaminants is lacking. The aim of the present in vitro study was to evaluate the quality and quantity of processing-related surface contamination of computer-aided design/computer-aided manufacturing (CAD/CAM) abutments in the state of delivery and after ultrasonic cleaning. A total of 28 CAD/CAM monotype and hybrid abutments were cleaned and disinfected applying a three-stage ultrasonic protocol (Finevo protocol). Before and after cleaning, the chemical composition and the contamination of the abutments were assessed using scanning electron microscopy (SEM), dispersive X-ray spectroscopy (EDX), and computer-aided planimetric measurement (CAPM). In the delivery condition, monotype abutments showed a significantly higher amount of debris compared to hybrid abutments (4.86 ± 6.10% vs. 0.03 ± 0.03%, p < 0.001). The polishing process applied in the laboratory after bonding the hybrid abutment components reduces the surface roughness and thus contributes substantially to their purity. The extent of contamination caused by computer-aided manufacturing of custom abutments can be substantially minimized using a three-stage ultrasonic protocol.