The aim of this thesis is to investigate the interaction of neutral atoms with conducting and superconducting surfaces. Experimental advances in the magnetic confinement of ultracold atoms have shown that they can act as a powerful tool in a wide range of phenomena such as electric and magnetic field imaging and matter wave interferometry. Coherent manipulation of atoms and ever smaller magnetic traps are essential elements in the implementation of integrated quantum devices for fundamental research, quantum information processing and precision measurements. This thesis considers main influences on atoms placed within three different environments which are useful in achieving miniaturization and efficient control in atomic magnetic traps: carbon nanotubes, dielectric surfaces and superconducting thin films. The possibility of holding atoms near the outside of a carbon nanotubes will be addressed. In order to give a qualitative analysis of the atom-nanotube interaction, thermally induced spin-flips and the Casimir-Polder potential have been considered. The comparison between these two effects is presented in this thesis. It indicates that the Casimir-Polder force is the dominant loss mechanism and an estimation of the minimum trapping distance is given based on its effect. Secondly, a first-principles derivation of spatial atomic-sublevel decoherence near dielectric and metallic surfaces will be presented. The rate obtained for the decay of spatial coherence has dual implications, on one hand, it can be considered as a measure of the coherence length of the fluctuations of the electromagnetic field arising from a given substrate. On the other hand, it turns out to be relevant for quantum information encoding in double well potentials. Finally, the known spin-flip transition rate will be linked to the flux noise spectrum in superconducting thin films showing the feasibility of using cold atomic clouds in the investigation of vortex dynamics.