According to the physical nature of the penetration of electromagnetic radiation, in different body's tissues, this process can be simulated with using Monte-Carlo (based on random number generation) methods. In this study penetration of ray in the muscle and bony tissues is simulated. With using Fortran90 code, the penetration of electromagnetic ray in the cube target was simulated. The curve of ray penetration in the muscle and bony tissues, for different ray energies (40, 60, 200, 500 KeV) is obtained. So change the output ray intensity is calculated per number of different primary rays. This calculation compared with experimental calculations in water, with comparing the results of code, that written by authors and experimental results, the results show good agreement with each other.