We report on the ablation depth control with a resolution of 40 nm on indium tin oxide (ITO) thin film using a square beam shaped femtosecond (190 fs) laser (λp = 1030 nm). A slit is used to make the square, flat top beam shaped from the Gaussian spatial profile of the femtosecond laser. An ablation depth of 40 nm is obtained using the single pulse irradiation at a peak intensity of 2.8 TW/cm2. The morphologies of the ablated area are characterized using an optical microscope, atomic force microscope (AFM), and energy dispersive X-ray spectroscopy (EDS). Ablations with square and rectangular types with various sizes are demonstrated on ITO thin film using slits with varying x-y axes. The stereo structure of the ablation with the depth resolution of approximately 40 nm is also fabricated successfully using the irradiation of single pulses with different shaped sizes of femtosecond laser.