Ultrafast laser-induced micro–nano hierarchical structures show broad applicability in optoelectronics, functional surfaces, and biomedicine. However, precisely controlling their formation through light field manipulation remains a relatively unexplored area. This work demonstrates a rapid drilling strategy on silicon using an emission-programmed, high-repetition-rate femtosecond Bessel beam. This spatiotemporal modulation enables a unique manufacturing synergy that integrates subtractive drilling and thermo-fluidic redistribution by the central lobes with additive nanostructuring by the peripheral lobes, directly fabricating a micro–nano hierarchical structure comprising tapered micro-holes, elevated micropillars, and dense nanocoatings. Meanwhile, areal scanning enables programmable geometry control through line interval adjustment. This approach offers new insights into laser-matter interactions and facilitates applications in infrared photodetection or drag-reduction surfaces.