In this thesis aberration corrected scanning transmission electron microscopy is employed to study the atomic structure of size-selected nanoclusters. The nanoclusters are produced using a magnetron sputtering gas aggregation cluster source with lateral time of flight mass filter, which enables the deposition of high precision samples. For Au nanoclusters, the combination of these techniques is used to determine atomic structure as a function of size, elucidate cluster growth mechanisms, determine the lowest energy structural isomers and investigate control of atomic structure through growth conditions. To further investigate the atomic structure of Au nanoclusters, an in-situ heating holder for the ac-STEM is used to extract a quantitative value for the energy difference between competing structural isomers. A study of surface melting of Au clusters on amorphous-carbon is also presented and the results are discussed with reference to several models for nanoscale melting. Finally, ac-STEM and STEM EELS are used to study the atomic structure and ageing in air of size-selected Ag nanoclusters. It is shown that exposure to air induces a change in both atomic structure and chemical composition.