Silicon material has been extensively used in electronics, optoelectronics, aerospace, biomedical and Microelectromechanical Systems (MEMS). In spite of good mechanical behaviour exhibited by the silicon material, their brittleness causes difficulty in machining, which greatly affects the surface integrity of the machined parts. The applicability of the ultrafast pulsed laser inscription technique to achieve high ablation depth on silicon wafer despite its higher surface reflectivity. A comparative study was carried out by fabricating microchannels of higher depth on uncoated and coated silicon wafer at various repetition rates. The formation of ablation depth, ablation width, surface roughness and amorphous layer thickness was taken as the standard for evaluating the effectiveness of the methodology. The underlying mechanism for the improved performance is due to the low temporal separation property of the ultrafast lasers.