Dynamic self-assembly of micropillars has found wide applications in targeted trapping, micro-crystallization and plasmonic sensing. Yet the efficient fabrication of micropillars array with high flexibility still remains a grand challenge. In this Letter, holographic femtosecond laser multi-foci beams (fs-MFBs) based on a spatial light modulator (SLM) is adopted to efficiently create micropillars array with controllable geometry and spatial distribution by predesigning the computer-generated holograms (CGHs). Based on these micropillars array, diverse hierarchical assemblies are formed under the evaporation-induced capillary force. Moreover, taking advantage of the excellent flexibility and controllability of fs-MFBs, on-demand one-bead-to-one-trap of targeted microspheres at arbitrary position is demonstrated with unprecedentedly high capture efficiency, unfolding their potential applications in the fields of microfluidics and biomedical engineering.