We demonstrate active pulse shaping using an Electro-Optic Modulator in order to compensate the pulse shaping effects caused by Gain Saturation in a high power Yb doped fiber amplifier chain and to generate various custom-defined output pulse shapes. Square, step and smooth pulse shapes are achieved, with mJ pulse energies. Use of a modulator to shape pulses rather than direct modulation of the diode drive current allows us to eliminate undesired transients due to laser start up dynamics. The required shaping is calculated based on a simple measurement of amplifier performance, and does not require detailed modeling of the amplifier dynamics.