A numerical model for computing scattering from a three-dimensional (3D) dielectric object above or below a rough interface is described. The model is based on an iterative method of moments solution for equivalent electric and magnetic surface current densities on the rough interface and equivalent volumetric electric currents in the penetrable object. To improve computational efficiency, the canonical grid method and the discrete dipole approach (DDA) are used to compute surface to surface and object to object point couplings, respectively, in O(N log N), where N is the number of surface or object sampling points. Two distinct iterative approaches and a preconditioning method for the resulting matrix equation are discussed, and the solution is verified through comparison with a Sommerfeld integral-based solution in the flat surface limit. Results are illustrated for a sample landmine detection problem and show that a slight surface roughness can modify object backscattering returns.