A study was conducted to demonstrate a method for producing structured polymer brushes of controlled morphology by carbon templating. A stable ultrathin template layer of carbonaceous material was locally deposited on an inorganic substrate by a focused electron beam. Amplification of the template by surface-initiated polymerization resulted in polymer brush layers of a controlled three-dimensional shape. These brushes were modified by polymer analogue reactions under extreme conditions such as nitration or sulfonation of polystyrene (PS) brushes, taking advantage of the high thermal and chemical stability of the grafting. The approach revealed that stable polymer brushes having all kinds of dimensions, architectures and chemical functionalities were prepared on various substrates. The gradual increase of the polymer brush thickness was found to be due to the increase of the polymer grafting density.