A method for precise multi-spot parallel ultrafast laser material structuring is presented based on multi-beam interference generated by dynamic spatial phase engineering. A Spatial Light Modulator (SLM) and digitally programming of phase masks are used to accomplish the function of a multi-facet pyramid lens, so that the laser beam can be spatially modulated to create beam multiplexing and desired two-dimensional (2D) multi-beam interference patterns. Various periodic microstructures on metallic alloy surfaces are fabricated with this technique. A method of preparing extended scale periodic microstructures by loading dynamic time-varying phases is also demonstrated. Scanning electron microscopy (SEM) reveals the period and morphology of the microstructures created using this technique. The asymmetry of interference modes generated from the beams with asymmetric wave vector distributions is equally explored. The flexibility of programming the period of the microstructures is demonstrated.