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Abstract We demonstrate a bottom-up process for programming the deposition of coaxial thin films aligned to the underlying dopant profile of semiconductor nanowires. Our process synergistically combines three distinct methods—vapor–liquid–solid nanowire growth, selective coaxial lithography via etching of surfaces (SCALES), and area-selective atomic layer deposition (AS-ALD)—into a cohesive whole. Here, we study ZrO 2 on Si nanowires as a model system. Si nanowires are first grown with an axially modulated n-Si/i-Si dopant profile. SCALES then yields coaxial poly(methyl methacrylate) (PMMA) masks on the n-Si regions. Subsequent AS-ALD of ZrO 2 occurs on the exposed i-Si regions and not on those masked by PMMA. We show the spatial relationship between nanowire dopant profile, PMMA masks, and ZrO 2 films, confirming the programmability of the process. The nanoscale resolution of our process coupled with the plethora of available AS-ALD chemistries promises a range of future opportunities to generate structurally complex nanoscale materials and electronic devices using entirely bottom-up methods.