Molecular-interaction-induced organizations are the basis of various biological and nonbiological systems. The molecular recognition process involved in the formation of such systems is rather complicated, as it constitutes a subtle balance of various noncovalent interactions. The molecular organization of electron-deficient aromatic systems is particularly appealing, as they are the potential candidates for a variety of applications. The main challenge in organizing aromatic moieties lies in controlling and optimizing the relatively strong π–π interactions by appropriate functionalization. Herein, we describe a simple molecular design involving phenylalanine methylester-functionalized naphthalenediimide (L-NDI and D-NDI) to achieve high-level molecular ordering by solution processing. NDIs are among the most promising organic n-type semiconductors. However the molecular ordering of these organic entities determines their optimal functioning in an organic device. Highly crystalline free-floating nanosheets with large lateral dimensions were obtained for the first time through molecularly engineered self-assembly of L-NDI and D-NDI systems. Interestingly the nanosheets exhibit a remarkable conductivity of 1.6 S cm−1. Furthermore the molecular organization of L-NDI was tuned into container-like complex architectures by employing chlorinated- co-solvent-mediated halogen bonding. The composition and the type of chlorinated co-solvent resulted in the formation of nanocups, mesocups, and bowl-like architectures. The nanocups possess a net volume of 0.1–1.5 attoliters (10−18 L) and can be used as containers for miniaturized applications.