Parallel processing in femtosecond-laser-based microfabrication is demonstrated using a microlens array in conjunction with a liquid-crystal spatial light modulator (SLM). A portion of the SLM is mapped onto each individual lenslet in the array and can be used to effectively switch foci on and off for fabrication. In addition, the technique allows for homogenizing the intensity of the array of foci and translating spots relative to their natural focus. The technique demonstrates the potential for high efficiency processing of aperiodic structures.