In this paper, the characterization and fluorescent labeling of silica rods are reported. These rods are synthesized following a recently reported method. Material properties of the silica rods measured with NMR, elemental analysis, TGA, and porosimetry are compared with those of well-established Stober silica spheres. Additionally, silica rods are made suitable for quantitative real-space studies by confocal microscopy. Several methods of fluorescent labeling to prepare rods with different fluorescent patterning, ranging from uniform fluorescence levels to gradients from one rod-end to the other, and even patterns of several colors are presented and discussed.