The effect of temperature on the noncontact atomic force microscopy (NC-AFM) surface imaging is investigated with the aid of molecular dynamics (MD) analysis based on the Sutton-Chen (SC) interatomic potential. Particular attention is devoted to the tip and sample flexibility at different temperatures. When a gold coated probe is brought close to the Au (001) surface at high temperatures, the tip and surface atoms are pulled together and their distance becomes smaller. The tip and sample atoms displacement varies in the different environment temperatures and this leads to the different interaction forces. Along this line, to study the effect of temperature on the resulting images, we have employed the well-known NC-AFM model and carried out realistic nonequilibrium MD 3D simulations of atomic scale imaging at different close approach positions to the surface.The environmental conditions such as moisture and temperature can have significant effects on NC-AFM images. In many applications, the fluid contaminant layer is considerably thicker than the range of the tip-sample interaction force gradient, and consequently attempts to image the true surface with NC-AFM fail. On the other hand, the environment temperature directly affects the interaction force, hysteresis, dissipated energy, and the cantilever bending (because of different top and bottom faces), and therefore it has a significant influence on the NC-AFM images. Tang et al. 4 investigated the effect of temperature and relative humidity on the patterning of a ferroelectric polymer poly (vinylidene fluoride-trifluorethylene) onto a gold substrate via dip-pen nanolithography (DPN). Recently, Roll et al. 5 reported measurements of the temperature dependence of dissipation in NC-AFM on a sample system of molecular crystallites of PTCDA on KBr. Additionally, Burke and Grutter 6 argued that the dissipation results obtained by Roll and co-authors 5 are often highly influenced by the tip structure, and the single sets of experimental data must be interpreted with caution. In a theoretical research, Trevethan et al. 7 studied the hysteresis as a function of system temperature for the MgO tip above the MgO surface at a specific distance. I another research 8 , they investigated the dependence of the dissipated energy, and the reversibility of a structural change, on the system temperature.Only a few papers can be found in literature dealing with the investigation of temperature effects on the interaction forces. For example, Kang and Kaburagi 9 carried out a theoretical analysis of the temperature effect on the interaction force between a single-atom tip and the substrate. They assumed that the temperature dependency arises from the change in phonon distribution of the substrate, and formulated the exerted force on the tip in terms of the Debye-Waller factor (DWF) within a single phonon process. Next they calculated the exerted force on the tip with several two-body potentials including Gaussian and Morse.As the main challenge of working at the nano-scale, understand...