This paper presents a novel method for fabricating nanopillar micropatterns for surface-directed liquid flows. It employs hybrid mask lithography, which uses a mask consisting of a combination of a photoresist and nanoparticles in the photolithography process. The nanopillar density is controlled by varying the weight ratio of nanoparticles in the composite mask. Hybrid mask lithography was used to fabricate a surface-directed liquid flow. The effect of the surface-directed liquid flow, which was formed by the air-liquid interface due to nanopillar micropatterns, was evaluated, and the results show that the oscillation of microparticles, when the micro-tool was actuated, was dramatically reduced by using a surface-directed liquid flow. Moreover, the target particle was manipulated individually without non-oscillating ambient particles.