The main purpose of this research was to investigate new medical applications of femtosecond laser ablation. A near-infrared femtosecond laser was tested and proved to be able to overcome the existing limitations and outperform the conventional long-pulse lasers in the areas of human urinary calculus (kidney stone) lithotripsy and skin treatment. The two primary objectives of my research are: 1) to investigate the feasibility of using femtosecond pulsed laser radiation to ablate urinary calculus of various compositions. The laser-calculus interaction mechanism was characterized using pump probe imaging and fast flash imaging. A novel fiber delivery system was developed to transmit and focus high energy femtosecond pulses for urinary calculus lithotripsy. The successful demonstration of the femtosecond laser lithotripsy provided a promising treatment method better than the existing long-pulse laser lithotripsy in a few different aspects, including less collateral damage to surrounding tissue, small-size debris and more controlled experimental condition. 2) to investigate the depth limitation of femtosecond subsurface ablation in scattering skin sample and develop a prototype tissue optical clearing device to enhance femtosecond beam penetration for deeper subsurface cavitation production in the skin. The successful demonstration of the device has potential benefits to new femtosecond-based therapies for reshaping or removing subcutaneous tissues. / text