We investigated area-selective atomic layer deposition (ALD) of zirconia (ZrO2) using a self-assembled monolayer (SAM) and atomic force microscopy (AFM) oxidation lithography as a method of fabricating nanostructures. A SAM layer was used as a chemical mask for the ZrO2 ALD process, and AFM oxidation lithography was used as a nanoscale patterning tool. AFM oxidation lithography was applied to create oxide patterns on octadecyltrichlorosilane SAM-grown silicon substrates. Subsequent HF etching removed the oxide patterns locally, exposing a silicon substrate underneath. After 100 cycles of the ALD process, ZrO2 ALD nanostructures similar to 7 nm high and sub-100 nm wide were fabricated with no detectable Zr element outside the pattern defined by AFM oxidation lithography. The present method makes it possible to construct advanced metal-oxide-semiconductor field effect transistor and quantum confinement structures with a wide range of ALD precursor materials.