This article presents a modified algorithm and a MATLAB-based program for computing the Moho topography, which uses the combination of the spatial domain technique and the FFT-based algorithm. The advantages of the algorithm are that it performs rapid computations with high precision, and the computation procedure does not need to use a low pass filter during iteration. The applicability of the proposed technique is demonstrated on three 3D synthetic and real gravity data from the Arabian Shield, Saudi Arabia. For the synthetic data cases, the obtained results are compatible with the assumed structures. Application on real data indicates that the result estimated by the proposed technique compares well with seismic data.