The tunneling-current signals which acquired by STM,include both the sample's molecular structure and the dynamic characteristics of STM system.The Short Time Fourier Transform(STFT) is utilized to estimate the power spectral density(PSD)of the tunneling-current signals and the data's feature vector was extracted in the frequency space.The results obtained by PSD estimation reveal that spectral-space-based feature vector can distinguish the interference from power line(50 Hz),and it can explain and analyze the dynamic characteristics of STM efficiently by using a damped harmonic oscillator model.Meanwhile,the recognition is helpful in the control of the practice scanning condition of STM and the 3-D recreation for the images of STM.