The aim was to examine the effect of retreatment process on the surface roughness and nickel titanium (NiTi) composition of ProTaper Universal Retreatment (PTUR; consists of 3 files; D1, D2, D3) and WaveOne Gold (WOG) (primary) instruments. Twenty extracted mandibular molar teeth with severe curved (30-40 degrees) mesial roots were selected and divided into two groups (n = 10) based on the instrument used for the removal of the root canal filling. Before and after using the instruments in two canals, they were subjected to atomic force microscopy (AFM) and energy dispersive X-ray spectrophotometry (EDX) analysis. The EDX analysis data and roughness average (Ra) and root mean square (RMS) values were analyzed statistically using a one-way analysis of variance and post hoc Tukey's test at the 5% significant level. There was no significant difference between the new and used D1 and D2 PTUR and WOG instruments in terms of the Ni composition (p > .05). The Ti contents of the used D2 and D3 PTUR instruments were lower those of the new instruments (p < .05). In both new and used instruments, PTUR and WOG have no difference in terms of Ra and RMS values. (p > .05). The Ra and RMS values of the PTUR and WOG systems significantly increased after removal of the root canal filling (p < .05). The use of PTUR and WOG instruments for removal of root canal filling in severely curved root canals affected the surface topography of the files. The NiTi composition of the WOG instruments was unaffected by the retreatment process.