The object of this thesis is the development of theoretical and experimental methods for the controlled manipulation of surfaces at the nanometer scale, including the design, construction and experimental demonstration of an atomic force microscope (AFM) based manipulator.

The transfer function description of an AFM system not only offers a theoretical dynamic characterization but, additionally, it is appropriate for the analysis of stability and controllability of different system configurations, i.e. different inputs and outputs. In this thesis, transfer functions are derived that correspond to a realistic model of the AFM sensor, including all its resonance modes and the tip-sample interaction. This theoretical description is then validated using the frequency response along an AFM cantilever.

Different experimental and control techniques have been combined in the NanoManipulator system to optimize AFM lithography. Optical video microscopy allows a fast recognition of the sample and exact positioning of the AFM tip in the particular region of interest, while UV-laser ablation offers the possibility of noncontact manipulation of a wide range of materials, including biological specimens. Two different control approaches have been implemented in the NanoManipulator system: (i) automated control using a vector-scan module, and (ii) interactive control based on the use of a haptic interface.

Using the NanoManipulator, the two different standard AFM lithography techniques based on dynamic methods (namely dynamic and modulated plowing) are compared by performing nanopatterning on thin resist films. The results reflect that modulated plowing, where the AFM tip is in permanent contact with the resist surface while the force is being modulated, offers the highest reliability, minimizing undesired side effects.

The isolation and extraction of localized regions of human metaphase chromosomes represents a promising alternative to standard methods for the analysis of genetic material. The NanoManipulator is an excellent tool for such application, as it is here illustrated by comparing AFM based mechanical dissection and noncontact ablation on side by side chromosomes. The results are analyzed in situ using AFM imaging, revealing the high precision of mechanical dissection.

Acoustical force nanolithography is a novel method for AFM based lithography where the cantilever is actuated using an acoustic wave coupled through the sample surface. The influence of acoustic wave frequency and magnitude, along with the preloading force of the cantilever are studied in detail. Acoustical force nanolithography can be used as a stand alone method or as a complement for the fine adjustment of manipulation forces.