Controlled growth of one-dimensional nanostructures is playing a key role in creating types of materials for functional devices. Here, we report procedures for controlled assembly of the dipeptide diphenylalanine (FF) into aligned and ultralong single crystals in a capillary. With the evaporation of solvent, nucleation of the crystal occurred in the confined region, and the crystal grew continuously with a supply of molecules from the concentration gradient system inside the capillary. Based on the "Knudsen regime", an ultralong aligned individual FF single crystal possessing an active optical waveguide property at macroscopic length scale could be obtained. Moreover, capillary is also an effective microdevice to investigate the disassembly process of the FF single crystals. This strategy has potentials to broaden the range of applications of aligned organic nanomaterials.