Neutron reflectivity has been used to investigate the porosity and surface roughness of three different liquid crystal alignment layers to elucidate how they orient the director. The absorption of hexane into these alignment layers was measured by neutron reflection and the volume fraction profile of the hexane within the layers was determined using the contrast variation method. Measurements were made on rubbed polyimide and silicon monoxide (SiO) evaporated at 5° and 30° to the substrate. The porosity and surface roughness of the alignment layers were found to be correlated with the induced pre-tilt of the director. The low pre-tilt rubbed polyimide and SiO 30° alignment layers were found to be smooth, uniform and impervious to hexane, whilst the high pre-tilt SiO 5° was porous and extremely rough. These observations suggest that both polyimide and SiO 30° rely on an anisotropic interaction with the surface rather than one induced by the surface topography. In contrast, the alignment of liquid crystals by SiO 5° probably originates from an interaction between the mesogens and the rough, porous surface.