The purpose of this study was to obtain a more precise estimate of the thickness of an atmospheric layer structure, based on the theoretical works of Chen and Chu (2001), using a modified dual-frequency interferometry method of MST radar. Horizontal layer structures in the atmosphere are frequently formed due to vertically confined refractivity irregularities. The thickness and position of a layer structure can be measured by Frequency Domain Interferometry (FDI) technique, using two or more carrier frequencies. The condition of a single-Gaussian layer is generally assumed to facilitate the mathematical manipulation in the FDI method but this rigorous condition is very difficult to satisfy due to multiple layers and varied atmospheric structures. Consequently, the thickness and position of a layer, obtained by the FDI method, may differ from true ones. Chen and Chu (2001) verified this, in results obtained from their theoretical/numerical examination. Moreover, they found various kinds of relationships between the thickness and position of a layer. These findings have been attributed to the coupling of various layer structures and the range weighting function of the radar system. The thickness-position relationship indicates that the estimated layer thickness might be closer to the true one at some places more than others, depending on the layer structure involved in the radar volume. This study examined dual-frequency observations carried out with the Chung-Li VHF radar, to reveal the prevailing thickness-position relationship and deduce the potential layer structure. In general, a thickness position relationship with a smaller thickness at the central height of the radar volume was obtained. This result was possibly due to multiple layers (more than two layers) or a single layer in company with significant background scatterers. According to numerical calculations, this kind of thickness-position relationship indicates that the thickness at the central height of the radar volume is closer to the true one. A quasi-linear relationship between layer thickness and radar pulse length was also observed, which demonstrated further that multiple layers and background scatterers have a significant impact on the thickness-position relationship of a layer. Since the radar volume for a short pulse length might contain just a single layer and fewer background scatterers, the data of 1-µs pulse length were adopted to estimate approximate layer thickness. Using this approximation and taking into account the thickness around the central height of the sampling gate, the estimated layer thicknesses were found to be around 30 meters and approximately 70% of them were smaller than 60 meters.