We present a novel polymer-chain-controlling and selective growth technique to make high-index-contrast (HIC) waveguides and photonic crystals. In the present work, poly-azomethine (poly-AM) films that are conjugated polymer were grown on substrates with surface treatment by chemical vapor deposition (CVD) using p-phenylenediamine (PPDA) and terephthalaldehyde (TPA) as reactive source monomers. For polymer chain controlling, poly-AM films were grown by CVD on SiO film, which was obliquely evaporated on a substrate tilted along the y-axis. The chains on the SiO film were found to be aligned along the y-axis. For selective growth, on a glass substrate surface, where a hydrophobic treatment was applied using hexamethyl-disilazane (HMDS), a hydrophilic SiO thin film was deposited through a metal mask by the vacuum evaporation to form a hydrophilic/hydrophobic pattern. The poly-AM thin film was found to be selectively grown on the SiO region, that is, on the hydrophilic region, without growth on the hydrophobic region. These results demonstrate a potentiality of the proposed technique to provide a wide range of three-dimensional fine structures.