In this article we study the effects of the wave number power spectrum of refractivity irregularities with anisotropic structures on the determination of the layer thickness and position by using the frequency domain interferometry (FDI) technique of MST radar returns. Numerical results show that both the power spectral form and the anisotropy of the refractivity irregularity contribute remarkably to the magnitude and phase of a two frequency cross-correlation function, provided that the radar beamwidth is not too narrow. By approximating the power law spectral form in the scattering integration equation to a modified Gaussian function, we propose a more realistic FDI expression for estimating the layer thickness and position. Furthermore, an FDI experiment at the Chung-Li coherent scatter 52-MHz radar was carried out on November 10, 1995. The radar data are used not only to calculate FDI coherence and phase but also to estimate the horizontal correlation length of the refractivity irregularities with conventional space antenna drift (SAD) method. Observational result shows that the horizontal correlation lengths are mostly within 10-40 m, indicating the anisotropic behavior of the irregularities. Substituting the observed values into the theoretical FDI expressions, we can obtain the layer thickness and position accordingly. By comparing the results of the proposed FDI expression with those of the existing FDI equations, we show that a large 50% difference in layer thickness estimation and tens of meters difference in layer position estimation are seen when vertical correlation length is assumed to be 3 m. These results suggest that the effects of the power spectral form and the anisotropy of the refractivity irregularity on the determination of layer thickness and layer position are significant and cannot be ignored.