Selective-area deposition of solid materials has been studied for the last two decades, mainly for the purpose of semiconductor device manufacturing. Combination of the selective-area processing with direct pattern writing on passivating masks by scanning probes and focused beams is expectedly a powerful technique for nanostructure formation. In this presentation, we report ultrathin multilayer masks which have been developed for selective-area chemical vapor deposition (CVD) of Si nanostructures. These masks have been tailor made in order to realize high-speed direct pattern writing as well as to ensure sufficient growth selectivity. Two successful examples of the ultrathin multilayer masks will be discussed. One is a SiHCl3-adsorbed SiO2 mask on which the patterns are drawn by utilizing electron stimulated desorption of Cl (sensitivity ~10 mC/cm2). A following CVD process forms polycrystalline Si selectively on the Cl-desorbed parts of the SiO2 surface [T.Yasuda et al, APL 76, 3203 (2000)]. Another example is a SiO2/ Si3N4 bilayer mask for which patterns are drawn by utilizing AFM-induced local oxidation of Si3N4 [F.S.-S.Chien et al, APL 76, 360 (2000)]. This mask is suited for epitaxial growth of various materials, and is compatible with high-temperature processing exceeding 1300 K [D.S.Hwang et al, JJAP 37, L1087 (1998)]. This study, partly supported by NEDO, was carried out at JRCAT under the joint research agreement between NAIR and ATP.