In this paper interaction of a different number of femtosecond laser pulses and various fluences with silicon wafer has been studied. Effects of the pulse number and the laser fluence on self-organized structures created during femtosecond laser pulses processing are investigated. The scanning electron microscopy images of the sample show that by increasing the number of laser pulses, spike-like structures form on the surface, which gradually transform to hills and holes structure. The increment of the laser fluence causes the microstructures to grow in diameter. However, the increase in diameter is limited by surface stability. When the micro-structures are at their maximum size and a stable geometrical shape, further fluence increment can cause new self-organized nanostructures to be created over the microstructures’ surface. The hierarchical micro and nanostructures created after femtosecond laser pulse interaction have a similar shape. Thus fractal-like structures formed in the femtosecond pulse laser processing can be useful in the surface nano-structuring applications.