We report nondestructive three-dimensional imaging and analysis techniques for material returned by the Stardust cometary collector. Our technique utilizes three-dimensional laser scanning confocal microscopy (3D LSCM) to image whole Stardust tracks, in situ, with attainable resolutions <90 nm/pixel edge. LSCM images illustrate track morphology and fragmentation history; image segmentation techniques provide quantifiable volumetric and dynamic measurements. We present a method for multipart image acquisition and registration in 3D. Additionally, we present a 3D deconvolution method for aerogel, using a theoretically calculated point spread function for first-order corrections of optical aberrations induced by light diffraction and refractive index mismatches. LSCM is a benchtop technique and is an excellent alternative to synchrotron X-ray computed microtomography for optically transparent media. Our technique, developed over the past 2 years, is a noninvasive, rapid technique for fine-scale imaging of high value returned samples from the Stardust mission, as well as various other samples from the geosciences.