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We have performed scanning tunneling microscopy (STM) in ultrahigh vacuum and transmission electron microscopy (TEM) on silver and gold clusters grown in preformed nanometer-sized pits on the surface of highly oriented pyrolytic graphite. We describe the preparation method and evaluate the three-dimensional shape of the clusters using a combination of STM and TEM applied to the same cluster sample. The nanometer-sized pits were essential to fix the clusters in position when using STM. The influence of the tip shape on the STM imaging of nanometer-sized clusters is discussed. © 1997 American Institute of Physics.