In this work, an aqueous acidic thin‐layer‐based strategy for fabricating nanostructures on silicon by using atomic force microscopy (AFM) nanolithography is presented. The approach involves the formation of microscale droplets via dilute hydrofluoride (DHF) etching, the conversion of the droplets to acidic thin layers by AFM‐probe scanning, and subsequent lithographic operations using a biased probe in the aqueous layers. By varying the concentration of the acidic DHF layers, the thin layers can facilitate the creation of both positive and negative patterns, such as oxide dots and Si pores, through anodic oxidation and dissolution. In particular, the anodic oxidation in the acidic media is associated with the field‐enhanced nonequilibrium dissociation of the weak electrolyte. The Si pore structure formation is related to the field‐assisted dissolution of anodic oxides and the Si substrate. The acidic‐layer‐based technique allows switching between different lithographic modes by changing the acidity of the DHF layers, and is complementary to bulk solution‐based and local meniscus‐based approaches in AFM nanolithography. In principle, this method can also be extended to other materials that have similar reactions with DHF.