The flow of supersonic plasma is accompanied by a highly thermalized region called the Magnetoshealth found after the bow shock. Enclosed within this region are different wave modes associated with classes of boundaries which have been determined by different methods. The efficacy of Hilbert-Huang transform (HHT) is based on the conditionality of allowing for the local analysis of frequencies, which presents the physical meaning of the original signal at that instant. The observed data have been taken from Cluster II Fluxgate Magnetometer (FGM) instrument that provides advantage for the analysis in three dimensions. The result compares favourably with instantaneous frequencies computed using simple Hilbert transform (SHT) with electric field measurements of Cluster II mission already carried out in literatures. The result of this study has shown that HHT provides the best applicability in the magnetosheath data analysis than the wavelet and Fast Fourier Transform (FFT). The application of HHT based on its advantages over other methods is viewed to be very critical in the analysis of multi-frequency signals where different frequencies could be determined distinctively at a point.