In this study, a new method coupling laser irradiation into a dual-beam scanning electron microscope (SEM) and focused-ion-beam (FIB) system is developed. By using a lensed fiber, pulsed laser illumination could be successfully delivered onto the sample under SEM imaging, providing in situ monitoring for laser material processing applications including local modification of micro-/nanostructures and laser-assisted chemical vapor deposition. In situ characterization of the laser-induced features by high resolution SEM imaging and energy dispersive x-ray spectrometry was successfully carried out. Furthermore, in situ repair of a contaminated lensed fiber probe during laser-assisted chemical vapor deposition was demonstrated via FIB milling. The results demonstrate the full compatibility of the lensed fiber apparatus with the dual-beam apparatus without disturbing the original functions of the system. The combination of guided laser radiation with SEM and FIB instruments offers a powerful capability for in situ monitoring of multilevel laser-based micro- and nanoscale material processing.