We successfully prepared controlled layers of NOBOW molecules on a variety of self-assembled monolayers (SAMs) such that the layers formed oriented domain structures in which the complex chiral/polar crystalline helical nanofilaments (HNFs) were arranged to form a B4 bent-core liquid crystal (LC) phase. The alignment of the B2 phase, which formed at a higher temperature than the B4 phase, affected the direction of the HNFs. The HNFs formed on the B2 smectic layers and were aligned parallel or perpendicular, respectively, to the substrates with high or low surface energies (molecule-philic or -phobic SAM-treated substrates). The HNFs confined within rectangular microchannels modified by the SAMs were directly visualized by electron microscopy and X-ray diffraction studies. The orientations of the HNFs were found to be governed by the B2 smectic layer morphology.