A soluble, asymmetric polydiacetylene has been shown to form stable monolayers at the air-water interface of a Langmuir trough. The monolayers of this unconventional amphiphilic polymer could be repeatedly deposited onto hydrophobic substrates during every upstroke cycle of the vertical dipping method to form uniform Z-type multilayers. Characterization of the precise orientation of the polymer main chain has been carried out to determine the spatial correlation between the nonlinear optical chromophore responsible for second-order nonlinear optical properties and the backbone. Polarized UV/vis and IR spectroscopic studies indicate a preferential orientation of the main chain along the dipping direction with a mean fluctuation of +/-30 degrees between director axis and chain trajectories. Polarization-dependent second-harmonic generation (SHG) in multilayers indicates a high degree of orientational anisotropy of the backbone. As expected, SHG intensities increase with the number of layers due to the noncentrosymmetric Z-type structure. The second-order nonlinear coefficient (d(33)) was estimated to be 1.52 pm/V at 1064 nm of Nd:YAG laser after correcting for absorption. Surface characterization and alignment of the extended chain backbones is further established using atomic force microscopy (AFM).