Size exclusion chromatography (SEC) columns pre-treated with a tetrabutylammonium bromide (TBABr) solution were used to develop a new method for extracting the microgel of Natural Rubber (NR). A solution of microaggregates smaller than 1 µm (Microgel<1µ) was obtained by collecting the corresponding elution volume after injecting the soluble fraction of the studied sample. The Microgel<1µ solution was then characterized by dynamic light scattering (DLS) and transmission electron microscopy (TEM). Direct imaging of two populations of isolated microaggregates with different sizes and structures was carried out. Spherical microaggregates with a hydrodynamic diameter (dh) of 500 nm were found to account for the majority of the isolated microaggregates. Larger microaggregates, with a dh of 1000 nm, were also observed and may have been formed by aggregation of the former. An “apparent molecular density” parameter was used to compare their compactness: the larger microaggregates were found to be 66% denser than the smaller ones.