We present here X-ray specular reflectivity (XRR) characterization of the ordering of Langmuir-Blodgett films of the liquid crystalline phthalocyanine (Pc) 2,3,9,10,16,17,23,34-octakis(2-benzyloxyethoxy)copper(II) phthalocyanine, 1, on Si(100) wafers with a native oxide layer and these same substrates modified with monolayers of varying percentages of methyl- and phenyl-terminated silanes. The central copper atom in these Pc's provides for high contrast in X-ray reflectivity for single-bilayer films of 1. The XRR data are modeled as arising from multiple layers of organic material, above and below the rows of copper atoms in the aligned Pc cores; variations in the total thickness of these films, and the spacing between the rows of copper atoms, are attributed to changes in the interaction with the substrate, and changes in the Pc orientation and side chain packing. The most pronounced effect on these parameters comes from variations in the ratio of the phenyl-silane versus methyl-silane content of the substrate modifiers and annealing of these films past their crystalline (K) --> liquid crystalline (LC) mesophase transition temperature. Transfer of multiple bilayers of this Pc leads to additional changes in the thickness of each layer, eventually forming a hexagonal close-packed array, reminiscent of bulk fibers of this material, as revealed by X-ray diffraction (XRD).