Nanodots forming dense assembly on a substrate are difficult to characterize in terms of size, density, morphology and cristallinity. The present study shows how valuable information can be obtained by a combination of electron microscopy techniques. A silicon nanodots deposit has been studied by Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM) to estimate essentially the dot size and density, quantities emphasized because of their high interest for application. High resolution SEM indicates a density of 1.6 × 1012 dots/cm2 for a 5 nm to 10 nm dot size. TEM imaging using a phase retrieval treatment of a focus series gives a higher dot density (2 × 1012 dots/cm2) for a 5 nm dot size. High Resolution Transmission Electron Microscopy (HRTEM) indicates that the dots are crystalline which is confirmed by electron diffraction. According to HRTEM and electron diffraction, the dot size is about 3 nm which is significantly smaller than the SEM and TEM results. These differences are not contradictory but attributed to the fact that each technique is probing a different phenomenon. A core-shell structure for the dot is proposed which reconcile all the results. All along the study, Fourier transforms have been widely used under many aspects.