The surface roughness of dental restorative materials has a crucial effect on the health of dental and periodontal tissues as well as for the longevity of restorations. In this study we tested a glass ionomer restorative cement, two nanohybrid resin composites, a flowable resin composite and a silorane-based composite. Twenty cylindrical specimens of each material were prepared, cured, polished and instrumented with a sonic scaler (Alegra ST ZE-55 RM W&H, Austria). The mean surface roughness was recorded using a profilometer (SJ-201, Mitutoyo, Japan) at three stages: before scaling, after scaling and after re-polishing. Additional specimens were analyzed by scanning electron microscopy and back-scattered imaging. Data were examined statistically by analysis of variance (ANOVA) and post-hoc tests at a level of significance of P < 0.05. The profilometric measurements and the SEM evaluation showed that, in most of the materials tested, the surface roughness was significantly increased after sonic instrumentation. After re-polishing the specimens, the roughness values were decreased. Periodontal scaling should include polishing of restorations in order to overcome alterations in surface roughness.