In civil engineering, roadway structure evaluation is an important application which can be carried out by ground penetrating radar. In this paper, firstly a signal model taking into account the influence of interfaces roughness (surface and interlayer) is proposed. In order to estimate the time delay and interface roughness, we propose a method composed of 2 steps: 1) a modified MUSIC algorithm is proposed for time delay estimation; 2) the interface roughness is estimated by using Maximum Likelihood method (MLE) with the estimated time delays. The proposed algorithms are tested on data obtained by a method of moments (MoM). Numerical examples are provided to demonstrate the performance of the proposed algorithm.