The application of ultrashort pulsed lasers for silicon scribing enables precise control of the ablation depth and generally reduces thermal side effects compared to ns-pulses. However, the formation of periodic holes with a depth of several µm can be observed at the bottom of the scribed trenches. The goal of this study is to investigate the influence of the pulse energy and the scan speed on the depth and average pitch of these holes. For this purpose, a simple model was developed to calculate the number of scans to achieve a specific cutting depth for different pulse energies and scan speeds. Then, wafers with a thickness of 525 μm were scribed to a depth of 50 µm using a fs-laser with a pulse duration of 380 fs and a wavelength of 520 nm. The pulse energy was increased from the minimum pulse energy necessary to achieve a scribing depth of 50 μm,1.6 μJ, up to 8 μJ. In addition, the scan speed was varied between 20 mm/s and 2000 mm/s. Finally, the wafers were broken along the cut and the side walls were investigated with scanning electron microscopy. It was found that the average pitch of the holes decreases and the depth of the holes increases with the pulse energy, while the scan speed has no influence. These findings suggest that the roughness at the trench bottom can be minimized by reducing the pulse energy to the minimum value necessary to achieve the desired cutting depth.