Silicon (Si) and its compounds are still actively being used by electronic and solar-energy industries. In this work, we focus on one-stop-instrument (OSI) for the characterization of silicon (Si)-based thin-films namely Si, silicon nitride (SiNx), and silicon oxide (SiO2). The goal of performing the characterization of Si-based compounds with OSI has been achieved by carrying out their nanoscale-characterization (Nano-Characterization) with a modern transmission electron microscope (TEM). The presented results demonstrate that TEM is proven to be a powerful OSI for carrying out the Nano-Characterization of Si-based multilayer stacks. It does that via electron microscopy imaging (EMI), and electron spectroscopic imaging (ESI) routes. The presented results show that while EMI allows imaging the structure and morphology of thin-films at nanoscale, the ESI, by combining imaging and spectroscopy techniques, enables distinguishing the pure Si regions from its oxide and nitride regions. Moreover, for the first time, we show that the ESI is sensitive enough to differentiate the crystalline Si regions from that of amorphous Si ones.