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A diesel particulate filter (DPF) is a key component for reduction of engine soot emission. The soot collected in the DPF is periodically burned off, so-called DPF regeneration, and a behavior of the pressure drop increased by the soot loading is generally utilized to estimate the amount, which must be a trigger of the regeneration. However, it is said that the estimation of the soot loading amount has considerable dispersion caused by two main reasons. One is hysteresis of the transient pressure drop resulted from the combination of so-called deep-bed and cake filtration modes. The other is a fluctuation of exhaust gas temperature and flow rate as well as a pulsation from the engine. In this study, the accurate estimation method of the soot amount accumulated in the DPF was proposed in combination with filtration layers (FLs) technology and a new algorithm based on fast Fourier transform (FFT) technology.