The quantum-dot cellular automata (QCA) scheme is a promising replacement for current CMOS technology. Patterning QCA molecules on a surface in a controlled manner is one of the fundamental research topics for the realization of room temperature operation of QCA computing. The water-soluble Creutz-Taube molecule [(NH3)5Ru(pyrazine)Ru(NH3)5](o-toluenesulphonate)5 (CT5), was successfully patterned on SiO2 surfaces by a new molecular liftoff technique. Patterned CT5 molecules formed as monolayers with two Ru atoms lying down on the surface. The finest CT5 nanolines demonstrated were around 15 nm after deconvolution of the tip size effect. For molecular nanopatterning, surface cleanliness is critical for molecular deposition and the investigation of deposited molecular patterns. Surface cleaning methods were compared before resist application on substrate surfaces. Dichloroethane (DCE) and dichloromethane (DCM) were found to be good polymethylmethacrylate (PMMA) removers and returned the surface to its original condition after PMMA removal. Contamination resist and octadecyltrichlorosilane (OTS) self-assembled monolayers (SAMs) resist were also investigated for nanopatterning of molecules. Compared with PMMA resist, both of these two resists are not appropriate for molecular nanopatterning. It is hard for SAMs to fully cover substrate surfaces and be removed after pattern transfer. It is time consuming to make contamination patterns because of the needed very large doses. For contamination resist, it is also very hard to control the contamination residual organic molecules in the SEM chamber. PMMA is the optimal resist for two reasons; one is the full coverage of substrate surface and the other is easy removal by DCE or DCM. For a complete scheme of the molecular liftoff technique for molecular nanopatterning, an inorganic resist, LiF (AlF3), is proposed to make nanopatterning of organic solvent-soluble molecules in the future. In order to obtain the real size of narrow molecular patterns and investigate surface defects affecting molecular adhesion, scanning tunneling microscopy (STM) is proposed to be used to solve these issues for the atomic resolution STM can provide.