High intensity near infrared femtosecond laser is a promising tool for three-dimensional processing of biological materials. During the processing of cells and tissues, long lasting gas bubbles randomly appeared around the laser focal point, however physicochemical and mechanical effects of the gas bubbles has not been emphasized. This paper presents characteristic behaviors of the gas bubbles and their contact effects on cell viability. High-speed imaging of the gas bubble formation with various additives in physiological medium confirms that the gas bubble consists of dissolved air, and amphipathic proteins stabilize the bubble surface. This surface protective layer inhibits interactions of gas bubbles and cell membranes. Consequently, the gas bubble contact does not cause critical effects on cell viability. On the other hands, burst of gas bubbles stimulated by an impact of femtosecond laser induced cavitation can lead to liquid jet flow that might cause serious mechanical damages on cells. These results provide insights for the parameter of biological tissue processing with intense fs laser pulses.