Clark MXR femtosecond (fs) laser micro structuring with pulse duration of 200fs up to a wavelength of 1030nm with a nominal frequency of 1 KHz on silicon wafer was studied in air using the direct focusing technique. The three steps of laser drilling process, namely hole entrance, spatter formation and hole exit, were conducted to investigate the laser parameters such as laser power, focus position, focus lens and number of pulses and their effects on the drilling hole geometry and spatter characteristic. The results show that the minimum entrance diameter is achieved while Zf =-0.2mm. It was easier for the laser to break through the material with longer lens focus length (f=100mm). However, smaller hole was produced when the focus length was shorter. The average diameter is as small as 23µm and aspect ratio is 1:30 at laser power of 200mW.