When the fast Hankel transform (FHT) filter technique is used to calculate the spatial-domain Green's functions for planar multilayered media, it can be difficult to obtain accurate numerical results because of branch-cut singularities and the surface-wave pole singularities. Although the singularities can be efficiently avoided through deforming the integration path of the Hankel transform from the real axis to the first quadrant in the complex plane, the argument of the integral kernel becomes a complex number so that the FHT filter algorithm cannot be directly applied. The modified FHT filter algorithm is proposed to overcome this problem by expressing the Bessel function with a complex argument as a sum of terms of product of Bessel function with the real part of the argument and Bessel function with the imaginary part of the argument. The FHT filter technique can then be applied to each expansion term. Numerical results confirm that the proposed approach has high accuracy and good efficiency in the near and intermediate fields. More importantly, it successfully extends the applicability of the conventional FHT method for general multilayered geometries.