In this study we use the double step gas cluster ion beam treatment to improve smoothing process of mechanically polished 4H-SiC (1000) wafers and compare it with conventional single-step smoothing. The first step is a higher energy treatment with 15 keV Ar cluster ions, and the second step is a lower 5 keV treatment. Single-step treatments are performed at 15 and 5 keV. It is shown that single-step 15 keV smoothing as compared with lower 5 keV one is very effective for removing the initial surface morphological feature (scratches), however, cluster ions impacting on the surface can create larger craters, resulting in roughness <i>R</i><i>_q</i> of 1.05 nm. Whereas, 5 keV treatment at a selected fluence cannot remove initial scratches, which requires using higher fluences, i.e. such smoothing becomes time consuming. On the other hand, crater morphology with such a treatment is less developed, hence, the roughness slightly decreases to 0.9 nm. Using the double-step treatment, one can obtain the surface with lower <i>R</i>_<i>q</i> roughness of 0.78 nm as compared with single-step treatment, at the same total cluster ion fluence. Therefore, the double-step treatment combines the advantages of the effective smoothing of scratches at high energy and smaller crater morphology at low energy. To evaluate the contribution of the cluster morphology introduced by the accelerated clusters into the total roughness, the cluster ion beam treatment of an atomically smooth 4H-SiC (1000) surface is also carried out. It is shown that the crater diameter increases in a range of 15–30 nm with the cluster energy increasing. More detailed analysis of the smoothing process is carried out by using two-dimensional isotropic PSD function. It is shown that the cluster treatment of mechanically polished 4H-SiC wafers effectively reduces the roughness in a wavelength range of 0.05–0.20 μm and the efficiency of smoothing is higher at higher cluster energy. In a range of 0.02–0.05 μm, a roughening effect is observed, which is due to the formation of craters. This roughening effect can be effectively reduced by the subsequent lower energy step treatment, which can be shown by the PSD function analysis of the smooth SiC surface treated initially by cluster ion beam.