Surface aligning agents, such as amphiphilic surfactants, are widely used to control the initial alignment of nematic liquid crystals (NLCs) in liquid crystal displays (LCDs). Generally, these agents are first coated on a substrate prior to NLC introduction. When mixed with NLCs, long alkyl chain amphiphilic agent additives may control the NLC alignment without requiring pretreatment because they may spontaneously form an adsorbed layer at the solid-NLC interface. These self-assembled layers (SALs) appear promising in the effective control of the initial alignment of LCDs. However, direct observation of the adsorbed layer structure in contact with the NLCs is challenging due to probe limitations. Furthermore, the areal densities and alignments of the amphiphiles adsorbed from NLCs at the solid-NLC interface are not previously reported. Herein, the structure of the surface aligning agent n-hexadecyltrimethylammonium-d42 bromide (d-CTAB) was investigated at the silicon-NLC interface using in situ neutron reflectometry (NR), which indicated that the CTAB self-assembled as a monolayer, with its alignment dependent on the amphiphile concentration. At low amphiphile concentrations, the alignment of the SAL and NLCs was parallel to the substrate. With increasing amphiphile concentration, the number of amphiphiles attached to the substrate increased within the framework of the Gibbs monolayer, with the alignment of the amphiphiles and NLCs becoming perpendicular to the substrate. The experimental setup used here is comparable to those of more natural systems, such as those found in the alignment of NLCs in LCDs.