A new template-directed method is described for controlling colloidal arrays by using capillary force. Surface relief gratings (SRGs) were used as a substrate for bottom layer induced crystal structure control. The crystal structure of each level of arrays was determined by the topology of SRGs and thermodynamic factors. The findings show that not only the ratio of SRG spacing to colloid diameter but also the ratio of SRG depth to colloid diameter affected the nature of the resulting crystal structure. When the ratio of SRG depth to colloid diameter was 0.74, a square array of colloids was well developed layer by layer. The second layer showed a unique dumbbell-like crystal structure. The method allows the formation of a well-organized body-centered cubic (bee)-like bottom mono- and bilayer and a wide top area of hexagonal array at a ratio of 0.48. This new method permits the control of wide crystal arrays of colloid particles even with a small diameter (350 nm) in a short time.