Self-assembled monolayers (SAMs) formed by chemisorption of n-alkanethiols (CH3(CH2)(n)SH) on films of gold permit manipulation of the mesoscale structure of nematic liquid crystals in contact with these surfaces. Mixed SAMs formed from CH3(CH2)(15)SH and either CH3(CH2)(4)SH or CH3(CH2)(9)SH homeotropically anchor nematic phases of 4-cyano-4'-pentylbiphenyl (5CB) and p-methoxybenzylidene-p-n-butylaniline (MBBA). Single-component SAMs, in contrast, do not uniformly anchor these nematic phases at room temperature: SAMs formed from CH3(CH2)(n)SH (2 < n < 15)cause either planar or tilted anchoring. Mixed SAMs that homeotropically anchor 5CB and MBBA are conformationally disordered, when characterized prior to contact with the liquid crystal, and have a low number density of long aliphatic chains. We conclude, however, that conformational disorder within the aliphatic chains of SAMs is not a sufficient condition to induce homeotropic anchoring because the aliphatic chains of single-component SAMs with n < 10 are fluidlike (conformationally disordered) at room temperature and do not homeotropically anchor nematic phases. We infer the number density of long aliphatic chains to be an important factor in the anchoring of liquid crystals on mixed SAMs. Self-assembled monolayers formed from n-alkanethiols, in combination with techniques for their patterning on surfaces, form the basis of a procedure to prepare micrometer-scale optical structures from liquid crystals.