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An approach has been developed to use atomic-force microscope (AFM) to pattern materials at the nanoscale in a controlled manner. By introducing a thermal-annealing process above the glass-transition temperature of poly (methylmethacrylate) (PMMA), the profile of indented nanopatterns has been dramatically improved by abatement of the tip-induced debris. This eliminates the main problem of the previous AFM-based tip-ploughing lithography method, namely the debris formation during the nanoplough and trench refilling by debris. We are able to reproducibly fabricate nanopatterns down to 40 nm. Meanwhile, the AFM-tip lifetime has been increased substantially. In particular, the adhesion between the PMMA layer on the edge of trenches and the substrate is significantly improved to enable reliable pattern transfer into GaAs/AlGaAs heterostructures by wet-chemical etching. Functional nanodevices with a lateral feature size of 100 nm to an etching depth of 70 nm are demonstrated using the method.