Particle patterning, referred to as colloidal patterning or natural patterning, has wide applications in the development of devices for photonic and surface-enhanced Raman spectroscopy applications. On the other hand, interfacial materials with special wettability properties have gained significant research interest over the past decade. In this study, we developed a self-assembly method for particle patterning using femtosecond (fs)-laser micromachined micro-concave arrays to modify surface wettability. Experimental results showed that arrays of micro-concave structures could reduce the water contact angle from 68° to 36°, thereby increasing the wettability of a surface and providing a uniform dispersion of polystyrene (PS) micro-particles. Subsequently, surfaces with different patterns consisting of these micro-concave structures were used to create more complex patterns of particles on silicon substrates; the patterned particles were able to be transferred to PDMS surfaces directly to create micro-particle templates on the flexible PDMS surface. This work provides new applications for fs-laser micro/nano processing and insights for the advancement of micro/nanoparticle self-assembly processes and transfer-printing in the future.