The aim of the present study is to evaluate the effects of 2% chlorhexidine and 5.25% sodium hypochlorite on the surface properties of Resilon cones with the atomic force microscopy. The Resilon cones were immersed in disinfecting agents (5.25% sodium hypochlorite and 2% chlorhexicline) at 1 and 5 min time intervals. Atomic force microscopy was used to evaluate topographical deviations of Resilon cones. Root mean square (RMS) parameters for topographic amplitudes were calculated. The cones exhibited statistically significant low RMS values at 5-min immersion in sodium hypochlorite and chlorhexicline groups compared to the all other groups (p < 0.05). One-minute immersion did not show any significant deterioration on the Resilon surface (p > 0.05). In conclusion, sodium hypochlorite and chlorhexicline solutions used for disinfection significantly decreased (p < 0.05) the RMS values of Resilon cones at 5-min applications.