This thesis describes the controlled growth of molecular nanostructures using modified metallic and semiconductor surfaces. The Ag/Si(lll)-(root3 x root3),the Sn/Cu(100) surface alloy system and the Bi/Si(100) nanolines and (2xn) surfaces were all investigated as suitable substrates for the controlled growth of pentacene, (C22H14) or trimesic acid, (C6H3(COOH)3) organic molecules. The following techniques were used in this study; Scanning Tunnelling Microscopy (STM), Low Energy Electron Diffraction (LEED), Normal Incident X-Ray Standing Waves (NIXSW) and Temperature Programmed Desorption (TPD). The room temperature growth and ordering of trimesic acid on the AgfSi(ll1)-(root3 x root3) surface was investigated. An oblique unit cell was determined and a model proposed for the highly ordered close-packed domains. The discovery of a new submonolayer phase on Sn/Cu(100) and the re-examined known phase are discussed. New models for these reconstructions are proposed. Adsorption of trimesic acid at room temperature on the clean substrate the lowest Sn coverage phase were studied. Two new Sn coverage dependent structures were discovered and bonding schemes in upright and flat orientations are discussed. BifSi(100)-(2xn) surface was exploited as a template for the ordered growth of pentacene, which exhibited orientation specific adsorption. The Bi/Si(100)-(2xn) single domain surface created on vicinal silicon was used to test the suitable of Daresbury 4.2 beamline for NIXSW Imaging experiments and the quality of the results are discussed.