The precision of laser-microsurgery is often limited by thermal and thermomechanical collateral damages. Adjusting the pulse width of the laser to the thermal relaxation time of the absorbing construction can avoid thermal side effects and facilitate a selective treatment of the selective cells. Conjugates of colloid gold and bovine intestinal alkaline phosphatase (AP) are presented as the model system for investigating protein inactivation in the vicinity of strongly absorbing nanoparticles, and under certain conditions the protein can be denatured and the membrane permeabliltiy can be increased with the irradiation of the nanosecond and picosecond laser. Calculations show that under irradiation of nano- or picosecond laser pulses gold particles of submicrometer size can easily be heated to several hundred kelvins, the thermal effects is confined in a space less than tens of nanometers. The mechanism of denaturalized protein is analyzed with this laser-based absorpting nanopartide technology.