The present study was designed to compare the nature of modified surface layers obtained by two different procedures on endodontic files made of NiTi alloy: the procedures were arc evaporation physical vapor deposition and thermal metal organic chemical vapor deposition (MOCVD). Experimental samples were GT Rotary Instruments. The first method was based on the physical deposition of elemental titanium in the presence of nitrogen. The second technique is a typical MOCVD procedure which adopts Ti(Et2N)4 as a titanium and nitrogen precursor. Control samples were not exposed to any process. The chemical composition of the surface and in-depth layers of each sample were examined by X-ray photoelectron spectroscopy and X-ray diffraction measurements. The instruments showed surface chemical compositions that were different from those seen in the control group; samples treated with the first method show a surface Nitrogen/Titanium ratio of 1; MOCVD instruments show a surface Nitrogen/Titanium ratio of 1.7; control samples show a Nitrogen/Titanium ratio of 0.2. Both techniques can produce a high nitrogen concentration on the surface. However, data showed that the morphologies, the in-depth nitrogen distribution, and the chemical nature of the coatings obtained with the two procedures were different. The paper also reports the effects of the two deposition procedures on the nickel/titanium ratio of the surface.