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Self-assembly of colloidal particles has an advantage of low cost, high productivity and applicability to various devices. The capability of assembling nano-scale particles on three dimensional structures can extend the fields of application, such as high-sensitivity gas sensors and bioassay devices with surface-functionalized particles. We demonstrate such assembly where monolayer polystyrene particles were assembled only on the sidewall of trenches etched on a silicon wafer. Moreover, it was found that the assembly structure can be controlled by the scallops when its periodicity is nearly the same as the particle diameter.