We report on the design and performance of a fiber laser system with adaptive acousto-optic macropulse control for a novel photocathode laser driver with 3D ellipsoidal pulse shaping. The laser system incorporates a three-stage fiber amplifier with an integrated acousto-optical modulator. A digital electronic control system with feedback combines the functions of the arbitrary micropulse selection and modulation resulting in macropulse envelope profiling. As a benefit, a narrow temporal transparency window of the modulator, comparable to a laser pulse repetition period, effectively improves temporal contrast. In experiments, we demonstrated rectangular laser pulse train profiling at the output of a three-cascade Yb-doped fiber amplifier.