Nanostructured peptide materials in ordered 3-D morphologies are promising in various applications including sensing, nanomedicine, and energy harvesting. Despite the significant progress in the fabrication of such materials, critical issues such as the role of amino acid sequence or protecting group anchoring the biomolecular structure on the formation of their ordered 3-D morphologies still prevent their further applications. In order to investigate the above points and to establish instructive engineering rules for the fabrication of 3-D bionanostructures, in this work, different biological molecules with varying numbers of phenylalanine units (single amino acid, H-Phe-NH2 to tetrapeptide H-Phe-Phe-Phe-Phe-OH) and various protecting groups (i.e., Boc, Fmoc) are studied. The thin films generated from these molecules are fabricated through a physical vapor deposition technique by engineering the deposition parameters. The results obtained indicate that H-Phe-Phe-OH, Boc-Phe-Phe-OH, and H-Phe-Phe-Phe-Phe-OH peptides generate vertically aligned, highly ordered 3-D bionanostructures, whereas H-Phe-NH2, Fmoc-Phe-OH, Fmoc-Phe-Phe-OH, and H-Phe-PhePhe-OH do not yield any distinctly ordered structure under the same deposition condition. Quantum chemical calculations suggest that while 2-D morphologies are dictated by both weak H-bonding and pi-pi stacking interactions, clusters that possess H-bonds as the primary interaction display a 3-D morphology. Our results provide not only a detailed understanding of the role of molecular structure of phenylalanine based peptides on the formation of ordered 3-D morphologies but also promising possibilities in the field of sensing and tissue engineering applications.