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Fabrication of semiconductor nanostructures by atomic force microscopy (AFM) is investigated. In our processing scheme, ultrathin photoresist layers are mechanically modified by an AFM tip with a subsequent pattern transfer by reactive ion or wet chemical etching. In combination with conventional optical lithography, this method allows the selective modification of micrometer scale patterns. Several parameters influence the size and shape of the nanostructures as well as the reliability of the process: the shape and the material of the tip, the thickness and hardness of the resist layer, the force applied to the tip, and the corrections of the scanner nonlinearities. Pattern transfer by reactive ion etching enforces a compromise between etch depth and resolution: Thinner resist layers allow the fabrication of smaller structures but inhibit a deep pattern transfer due to the limited resistance of the photoresist to sputtering. Application of our mask-based lithographic process for the fabrication of Si, SiGe, and GaAs nanostructures is demonstrated. © 2000 American Institute of Physics.