Sophisticated transmission electron microscopes (TEM) could be used to monitor transformations of carbon nanomaterials at the atomic level under an electron beam. When the electron beam possesses sufficient energy to displace carbon atoms from lattices, vacancies and interstitials are created. Therefore, under specific beam conditions, one is able to create reactive sites (vacancies or divacancies) and reactive atoms (ad-toms or interstitials), that could start interacting between themselves or with other nanoparticles. In this talk, we study from the theoretical and experimental standpoint, the effects of high electron irradiation at elevated temperatures on single-walled carbon nanotubes (SWNTs). Under these conditions, we witnessed the “welding” of SWNTs exhibiting various geometries. The nanotube welding mechanism is based on the formation and reconstructions of vacancies and divacancies, under the high electron beam, that result in the formation of molecular junctions involving 7 or 8 membered carbon rings. We will also show that controlled electron irradiation of MWNTs filled with metal nanowires, could cause large pressure buildup within the nanotube cores, to the extent of being able to plastically deform, extrude, and break the solid materials that are encapsulated inside. The pressure buildup is based on the creation and reconstruction of vacancies and divacancies that result in shrinkage of the tube diameter, which induces a compression of the encapsulated metals. However, when these vacancies are created, the displaced carbon atoms (interstitials) become very reactive and they could also be embedded in the encapsulated metal particle cores, which subsequently emerge as single- or multi-walled nanotubes inside the host nanotubes. These observations at atomic resolution in an electron microscope indicate that bulk diffusion of carbon through the body of catalytic particles is the nanotube growth-limiting process. When we combine electron irradiation effects and Joule heating we have been able to produce stable metal-nanotube heterostructures exhibiting covalently bonded interfaces between metal and carbon atoms. We will discuss that the electronic transport along these heterostructures is enhanced and it is due to the presence of covalent bonds established between the metal and the carbon atoms. Finally, novel results regarding the edge carbon atom reconstruction of graphene nanoribbons under electron beam irradiation and Joule heating, will be visited. It is clear that these in-situ TEM experiments lead to the observation of reactions at the atomic level that have never been witnessed, and therefore, much more needs to be achieved along this direction when dealing with carbon nanostructures and other chemical species, so as to control atomic and nanostructure manipulation towards the controlled fabrication of nanodevices.