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In situ experiments, based on electron irradiation at high temperature in a transmission electron microscope, are used to investigate isolated, packed and crossing single-wall nanotubes. During continuous, uniform atom removal, surfaces of isolated single-wall nanotubes heavily reconstruct leading to drastic dimensional changes. In bundles, coalescence of single-wall nanotubes is observed and induced by vacancies via a zipper-like mechanism. "X", "Y", and "T" carbon nanostructures are also fabricated by covalently connecting crossed single-wall nanotubes in order to pave the way toward controlled fabrication of nanotube based molecular junctions and network architectures exhibiting exciting electronic and mechanical behavior. Each experiment is followed by quantum modeling in order to investigate the effect of the irradiation process at the atomic level.