To observe the fine distribution of minor aluminum and germanium dopants in the erbium-doped fiber (EDF) core of an optical amplifier, a sample thinning technique was applied for field emission electron probe microanalysis (FE-EPMA) together with wavelength-dispersive X-ray spectrometry. This technique significantly improved the spatial resolution without much degradation of the minimum detection limit for FE-EPMA. As such, this enabled us to observe the distribution of minor dopants in EDF. Moreover, we propose a very simple sample preparation to prevent electron-beam radiation damage, a problem involved with FE-EPMA of low-conductivity materials such as SiO2 glass, which is the main component of EDF.