We investigate the effect of preparation parameters on the formation of microstructures created on a single crystal silicon wafer covered with a polyethylene terephthalate (PET) transparent film by femtosecond pulse laser with a central wavelength of 800 nm. The results reveal that formation of the cone microstructures depends on laser fluence, and the cone microstructures cannot be created by lower laser fluence or can be destroyed by higher laser fluence. The laser scanning speed can directly affect the quality of the cone microstructures, and lower speed will destroy the cone, while higher speed will create indistinct cone microstructures each with smaller depth. Some idealized structures are obtained by optimizing the experimental parameters. Finally, we find that the cone microstructures on silicon wafer covered with a film are caused by both laser ablation and oxidation, and laser ablation plays a major role.