A novel method to produce a multifunctional microarray in which different types of self-assembled monolayers (SAMs) are positioned on predefined surface sites on an oxide-covered silicon substrate is described. To achieve this, a liquid-transportation system called “liquid manipulation lithography” (LML) is developed. This system allows the delivery of different varieties of molecular inks, trialkoxysilanes, onto each predefined surface position of the given substrate even under ambient conditions. Under optimum conditions, the transferred trialkoxysilane inks first form one-molecule-thick microstructures at each surface position through the hydrolysis of the reactive silanes with surface water adsorbed on the substrate, followed by a condensation reaction. Three types of trialkoxysilanes with long alkyl-chains, specifically triethoxysilylundecanal (TESUD), N-(6-aminohexyl)-3-aminopropyltrimethoxysilane (AHAPS), and octadecyltrimethoxysilane (OTS), are used as model molecular inks due to their high-end group-functionalities in biological and electronic applications. The precise positioning of the ink with sub-micrometer edge resolution is performed by carefully controlling a femtoliter-scale liquid-injection micromanipulator under a microscope. To ensure that the prepared SAM microarray is available for parallel analysis of biomolecular interactions, the area-selective immobilization of a protein molecule is explored. Successful observation of the area-selective biomolecular attachment confirmed a high industrial potential for the method as a lithography-free process for the miniaturization of a multifunctional SAM array on an oxide substrate.