Here dynamic mode Scanning Thermal Microscope (SThM) nanomachining technique is presented. The hypothesis states that “Excitation on the base can control the depth of nanomachining process by SThM probe”. The mathematical model is determined based on the Euler-Bernoulli beam. Partial differential equation of motion is solved by separating variables for linear equations and assumed modes method for nonlinear equations. Thermal vibrations is associated with a temperature dependent axial force. Constant, linear and quadratic temperature distribution over the probe are investigated while the probe is harmonically excited on the base at its approximated fundamental resonance frequency. The shifted resonance frequencies and amplitude of response in the excited frequency and shifted resonance frequencies are determined. The results indicate that temperature difference shifts the resonance frequencies, and its influence on vibration amplitudes are significant. It is explained that the effect of temperature distribution function is significant on resonance frequencies shift but negligible on amplitudes. It is showed, the amplitude is decreased in all frequencies with increasing the temperature difference. Finally it is demonstrated that with adding a known excitation on the base the depth of nanomachining process can be controlled. It is declared increasing the temperature improves the quality of final nanomachined surface. Keywords: Scanning thermal microscope, Base excitation, Nanomachining depth, Shifted resonance frequency, Probe response amplitude, Surface finish