Roughly 4.6 billion years ago our solar system’s precursor materials were formed from a vast molecular cloud according to astronomical and meteoritical observations and theory. In recent decades some of the best clues regarding this early history were achieved through the study of interplanetary dust particles (IDPs) collected by aircraft in the Earth’s stratosphere. The non-terrestrial portion of the particle population represent fragments of both comets and asteroids. IDPs therefore differ from the meteorite collection that represent only asteroids, plus a few larger planetary bodies. IDPs carry valuable information about comets, a class of solar system bodies whose orbits that take them beyond the outer planets. When comets pass through the inner solar system they eject solids owing to volatile ice interaction with intense solar radiation. This interaction forms the well-known visible cometary coma, or tail. Until just a few years ago the study of IDPs has been the only direct link to determining the compositional nature of comets. Recently, we have had the opportunity to examine cometary material with provenance brought back to Earth by NASA’s Stardust mission from a known source. The Stardust spacecraft collected thousands of solid particles during a fly-by of comet Wild 2 in 2004 and returned this valuable payload to Earth in 2006. Samples collected in silica aerogel collection tiles have been extracted, sectioned, and examined with a field emission scanning electron microscope (SEM) using scanning transmission electron microscopy (STEM) and scanning transmission Xray microanalysis by energy dispersive spectrometry (STEM-EDS) in the SEM. Spot analyses of cometary nanoparticles and their matrix collected by beam deflection are presented along with X-ray spectrum imaging results of fine-scale mixtures of cometary materials and aerogel. Strategies for unraveling the complexity of the system using high spatial resolution analysis in the SEM are presented.