Steady-state visual evoked potential (SSVEP) signal collected from the scalp typically contains other types of electric signals, and it is important to remove these noise components from the actual signal by application of a pre-processing step for accurate analysis. High-pass or bandpass filtering of the SSVEP signal in the time domain is the most common pre-processing method. Because frequency is the most important feature information contained in the SSVEP signal, a technique for frequency-domain filtering of SSVEP was proposed here. In this method, the time-domain signal is extended to multi-dimensional signal by empirical mode decomposition (EMD), where each dimension represents a intrinsic mode function (IMF). The multi-dimensional signal is transformed to a frequency-domain signal by 2-D Fourier transform, the Gaussian high-pass filter function is constructed to perform high-pass filtering, and then the filtered signal is transformed to time domain by 2-D inverse Fourier transform. Finally, the filtered multi-dimensional intrinsic mode function is superimposed and averaged as the frequency-domain filtered signal. Compared with the time-domain filtering method, the experimental results revealed that frequency-domain filtering method effectively removed the baseline drift in signal and effectively suppressed the low-frequency interference component. This method was tested using data from public datasets and the results show that the proposed frequency-domain filtering method can significantly improve the feature recognition performance of canonical correlation analysis (CCA), filter bank canonical correlation analysis (FBCCA), and task-related component analysis (TRCA) methods. Thus, the results suggest that the application of frequency-domain filtering in the pre-processing stage allows improved noise removal. The proposed method extends SSVEP signal filtering from time-domain to frequency-domain, and the results suggest that this analysis tool significantly promotes the practical application of SSVEP systems.