The aims of this in vitro study are to compare the efficacy of different cleaning methods in removing debris of failed implants and to detect thermal changes of the implants treated by various scaling instruments. Twenty-seven failed implants and two unused implants as control were included to this study—group 1: plastic curette (P), group 2: titanium curette (T), group 3: carbon curette (C), group 4: titanium brush (TB), group 5: Er:YAG laser (laser 1 (L1) 100 mJ/pulse at 10 Hz), group 6: Er:YAG laser (laser 2 (L2) 150 mJ/pulse at 10 Hz), group 7: Er:YAG laser (laser 3 (L3) 200 mJ/pulse at 10 Hz), group 8: ultrasonic scaler appropriate for titanium (US), group 9: air abrasive method (AA) + citric acid, and group 10: implantoplasty (I). The changes on the treated/untreated titanium surfaces and remnant debris were observed by scanning electron microscopy (SEM). Temperature of the implants before and after treatment was detected using a thermocouple. The use of air abrasive and citric acid combination and Er:YAG laser groups was found as the best methods for the decontamination of titanium surfaces of failed implant. When the hand instruments were compared, titanium curette was found better than both the plastic and the carbon curettes which leave plastics and carbon remnants on the titanium surface. The temperature was higher after hand instrumentation when compared to other experimental groups (p < 0.05). Within the limitations of the present in vitro model, it can be concluded that the best method for decontamination of the implant surface is the use of air abrasives and Er:YAG laser.