The influences of substrate roughness, order in the surface functionalization monolayer, and the alkylbis(phosphonate) chain length on the structural order of hafnium-alkylbis(phosphonate) multilayer films were investigated using external reflectance Fourier transform infrared (FTIR) spectroscopy. To examine the effects of substrate roughness, multilayers of hafnium-decylbis(phosphonate) (Hf-C10BP) were grown on as-evaporated gold films and on similar films which were flame-annealed. The influence of alkyl chain order in the surface functionalization monolayers was investigated by preparing Hf-C10BP multilayer films on monolayers of 4-mercaptobutylphosphonic acid (SC4P) and 12-mercaptododecylphosphonic acid (SC12P). Effects of the bis(phosphonate) alkyl chain length on alkyl chain order in multilayer films were examined by assembling multilayer films using hafnium and alkylbis(phosphonic acids) with 6-, 8-, 10-, and 12-carbon chain lengths (C(n)BPA). FTIR spectra indicate that annealing of the gold substrate prior to functionalization and self-assembly does not significantly affect the order of the alkyl chains in the multilayers. While the IR spectra of SC12P anchor monolayers indicate the alkyl chains are better ordered than monolayers of SG(4)P, the order of the alkyl chains in the Hf-C10BP multilayers grown on the two anchor monolayers is very similar and is less than that of the SC12P monolayer. The overall degree of alkyl chain order in the multilayers is dependent on the bis(phosphonate) chain length. Chain order decreases as the alkyl chain of the bis(phosphonate) becomes shorter; films grown with C(5)BPA show essentially liquid-like disorder, indicating that an eight-carbon alkyl chain is the lower limit for producing multilayers with some crystallinity in the alkyl chains of the organic layers.