A localized nanostructure growth apparatus that has a partitioned chamber is provided, where a first partition includes a scanning probe microscope (SPM) and a second partition includes an atomic layer deposition (ALD) chamber, where the first partition is hermetically isolated from the second partition, and at least one SPM probe tip of the SPM is disposed proximal to a sample in the ALD chamber. According to the invention, the hermetic isolation between the chambers prevents precursor vapor from damaging critical microscope components and ensuring that contaminants in the ALD chamber can be minimized.