Ultrashort pulsed laser polymer processing has attracted much interest recently.Ultrashort pulsed laser has an advantage in the processing of transparent and dielectric materials due to its high intensity and short pulse duration. Many investigations have been conducted in this area. However, there are still important issues yet to be clarified and resolved. These include a rigorous and quantitative investigation on the nonlinear absorption of laser power by the irradiated substrate, the associated thermal effects and heat conduction on the transparent materials (e.g. a transparent polymer). In addition, it is known that a short pulsed laser could modify the surface wettability of a polymer, but the linkage of the modification to nonlinear absorption has never been correlated. Polystyrene (PS) is a versatile polymer with many applications; many of these applications can take advantage of the different wettability if available. As PS is transparent to the wavelength of femtosecond laser employed for this investigation, PS is a natural choice for the current investigation.In the current study, the nonlinear absorption behavior of thick transparent PS samples were theoretically analyzed and experimentally investigated by applying the z scan technique. The thick PS sample was treated as a stack of thin samples and the nonlinear absorption behavior at different laser powers were investigated. The nonlinear absorption coefficient of PS was quantified to be 0.000695 m/W. The absorbed laser energy by the PS substrate will subsequently be converted to heat energy, and be conducted away. This femtosecond laser induced thermal effects