An extension of empirical mode decomposition (EMD) is proposed in order to make it suitable for operation on trivariate signals. Estimation of local mean envelope of the input signal, a critical step in EMD, is performed by taking projections along multiple directions in three-dimensional spaces using the rotation property of quaternions. The proposed algorithm thus extracts rotating components embedded within the signal and performs accurate time-frequency analysis, via the Hilbert–Huang transform. Simulations on synthetic trivariate point processes and real-world three-dimensional signals support the analysis.