Influence of low and medium energy electron beam (E-beam) irradiation on the single-walled (SW) and multiwalled (MW) carbon nanotube films grown by microwave chemical vapor deposition are investigated. These films were subjected to electron beam energy of 50 keV from scanning electron microscope for 2.5, 5.5, 8.0, and 15 h and 100, 200, and 300 keV from transmission electron microscope electron gun for a few minutes to approximately 2 h continuously. To assess the surface modifications/structural degradation, the films were analyzed prior to and post-irradiation using x-ray diffraction and micro-Raman spectroscopy in addition to in situ monitoring by scanning and high-resolution transmission electron microscopy. A minimal increase in intertube or interplanar spacing (i.e., d002) for MW nanotubes ranging from 3.25–3.29 Å (∼3%) can be analogized to change in c-axis of graphite lattice due to thermal effects measured using x-ray diffraction. Resonance Raman spectroscopy revealed that irradiation generated defects in the lattice evaluated through variation of: the intensity of radial breathing mode (RBM), intensity ratio of D to G band (ID/IG), position of D and G bands and their harmonics (D* and G*). The increase in the defect-induced D band intensity, quenching of RBM intensity, and only a slight increase in G band intensity are some of the implications. The MW nanotubes tend to reach a state of saturation for prolonged exposures, while SW transforming semiconducting to quasi-metallic character. Softening of the q = 0 selection rule is suggested as a possible way to explain these results. It is also suggestive that knock-on collision may not be the primary cause of structural degradation, rather a local gradual reorganization, i.e., sp2+δ ⇔ sp2+δ, sp2 C seems quite possible. Experiments showed that with extended exposures, both kinds of nanotubes displayed various local structural instabilities including pinching, graphitization/amorphization, and forming intra-molecular junction (IMJ) within the area of electron beam focus possibly through amorphous carbon aggregates. They also displayed curling and closure forming nano-ring and helix-like structures while mending their dangling bonds. High-resolution transmission electron microscopy electrons corroborated these conclusions. Manufacturing of nanoscale structures “nano-engineering” of carbon-based systems is tentatively ascribed to irradiation-induced solid-state phase transformation, in contrast to conventional nanotube synthesis from the gas phase.