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In laser clinical applications, the process of photon absorption and thermal energy diffusion in the target tissue and its surrounding tissue during laser irradiation are crucial. Such information allows the selection of proper operating parameters such as laser power, and exposure time for optimal therapeutic. The Monte Carlo method is a useful tool for studying laser-tissue interaction and simulation of energy absorption in tissue during laser irradiation. We use the principles of this technique and write a new code with MATLAB 6.5, and then validate it against Monte Carlo multi layer (MCML) code. The new code is proved to be with good accuracy. It can be used to calculate the total power absorbed in the region of interest. This can be combined for heat modelling with other computerized programs.