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This work reports on the electron microscopy analysis of the structure and morphology of gold nanoparticles produced by ion implantation as well as their relationship to their optical properties. Metalic nanoparticles by ion implantation are usually spherical and formed beneath the surface of a dielectric matrix. In this experiment, the matrix was sapphire. After high-energy Si ion irradiation, the gold nanoparticles were elongated into prolate spheroids. Since the nanoparticles are embedded in a dielectric matrix, secondary electron imaging in a JEOL JSM-7800F at low voltage did not allow their analysis. This work proposes an analysis using backscattered electron imaging in a field emission scanning electron microscopy at higher voltages (20 kV) to explore the morphology of the embedded nanoparticles. The samples were observed by cross-sectional view as well as a top view of the surface of the sapphire matrix for exploration and recognition of their morphology, dimensions, distribution, and composition. The analysis was extended by means of Rutherford backscattering spectrometry, X-ray diffraction, and optical extinction spectroscopy. The nanoparticles exhibited structural and optical properties correlated directly to the morphology observed by microscopy. The beam interaction with the sample and the used parameters was simulated in the CASINO code, from which the depth of exploration with distinct parameters used in microscopy analysis was estimated.