A nanopillars array for the application of molecular controlling was fabricated by use of focused ion-beam (FIB) fine milling on a substrate of silicon. The nanopillars array can realize cell/ molecular adhesion and movement control by the arrays high-density contact dots and tiled cone angle of the pillars. This can be obtained using FIB with two methods. One is direct fine milling with bitmap function, and the other is zero-overlap scanning in both directions of horizontal and vertical alternatively with a stage in a certain tilted angle. The milling process was investigated under different beam current and the stage-tilting angles, which determines an aspect ratio and the inclined angle of the pillars. In order to characterize the nanopillars array, we made a replica of the nanopillars array by aid of nanoimprinting with poly(dimethylsiloxane) (PDMS), and measured the replica by atomic force microscope (AFM). The pillars array can be used as a molecular manipulator to cause cell/molecular motion forward in only one direction. This motion cannot be backward. It will also be helpful for cell/molecular analysis, such as molecule separation and purification, molecular detection, DNA hybridization, etc. (c) 2005 American Vacuum Society.