The benefits of short pulse (femtosecond) laser machining over conventional nanosecond lasers have been well demonstrated: higher aspect ratio features with smaller remelt zones and less recast material. However, shock induced defects can degrade the mechanical, electrical and optical properties of the remaining material, especially in brittle materials. Our focus is to reduce the amount of defects created while maintaining the machining advantages of using ultra-short pulses. Utilizing a chirped pulse amplified Ti:Sapphire laser with a pulse energy of 1 mJ and a pulsewidth of 120 fs we investigated the effects of pulsewidth, laser frequency and pulse energy on the controlled micro-ablation of Kovar and silicon films. Hole morphology and diameter were characterized by SEM. Hole depth was measured by laser profilometry. Hole volumes were determined by a combination of profilometry and SEM to determine the rate of material removal. The ablation thresholds for both Kovar and Si are between 200–300 mJcm−2.