The electronic and optical characteristics of molybdenum disulphide (MoS2) film significantly vary with its thickness, and thus a rapid and accurate estimation of the number of MoS2 layers is critical in practical applications as well as in basic researches. Various existing methods are currently available for the thickness measurement, but each has drawbacks. Transmission electron microscopy allows actual counting of the MoS2 layers, but is very complicated and requires destructive processing of the sample to the point where it will no longer be useable after characterization. Atomic force microscopy, particularly when operated in the tapping mode, is likewise time-consuming and suffers from certain anomalies caused by an improperly chosen set point, that is, free amplitude in air for the cantilever. Raman spectroscopy is a quick characterization method for identifying one to a few layers, but the laser irradiation causes structural degradation of the MoS2. Optical microscopy works only when MoS2 is on a silicon substrate covered with SiO2 of 100~300 nm thickness. The last two optical methods are commonly limited in resolution to the micrometer range due to the diffraction limits of light. We report here a method of measuring the distribution of the number of MoS2 layers using a low voltage field emission electron microscope with acceleration voltages no greater than 1 kV. We found a linear relationship between the FESEM contrast and the number of MoS2 layers. This method can be used to characterize MoS2 samples at nanometer-level spatial resolution, which is below the limits of other methods.