Ultra-wideband pulse radar exhibits high range resolution, and excellent capability in penetrating dielectric media. With that, it has great potential as an innovative non-destructive inspection technique for objects such as human body or concrete walls. For suitability in such applications, we have already proposed an accurate permittivity estimation method for a 2-dimensional dielectric object of arbitrarily shape and clear boundary. In this method, the propagation path estimation inside the dielectric object is calculated, based on the geometrical optics (GO) approximation, where the dielectric boundary points and its normal vectors are directly reproduced by the range point migration (RPM) method. In addition, to compensate for the estimation error incurred using the GO approximation, a waveform compensation scheme employing the finite-difference time domain (FDTD) method was incorporated, where an initial guess of the relative permittivity and dielectric boundary are employed for data regeneration. This study introduces the 3-dimensional extension of the above permittivity estimation method, aimed at practical uses, where only the transmissive data are effectively extracted, based on quantitative criteria that considers the spatial relationship between antenna locations and the dielectric object position. Results from a numerical simulation verify that our proposed method accomplishes accurate permittivity estimations even for 3-dimensional dielectric medium of wavelength size.