To compute the greatest common divisor (GCD) of a set of multivariate polynomials, modular algorithms are typically employed to prevent any growth in the coefficient polynomials in the intermediate expressions. However, when dealing with multivariate polynomials with a priori errors on their coefficients, using such modular algorithms becomes challenging. This is because any resulting approximate GCD computed in one variable may have perturbations depending on the evaluation point and may not be an image of the same desired multivariate approximate GCD. This necessitates computing it as given multivariate polynomials, and operating with large matrices whose size is exponential in the number of variables. In this paper, we present a new modular algorithm, suitable for dense cases and effective for sparse ones, called “SLRA interpolation”. This algorithm uses the multidimensional fast Fourier transform (FFT) and the structured low-rank approximation (SLRA) of non-square block diagonal matrices. The SLRA interpolation technique may reduce the time-complexity for one iteration in the computation of approximate GCD of several multivariate polynomials, especially for the sparse case.