In contrast to small molar mass compounds and organic macromolecules, detailed structural investigation of inorganic-organic core-shell nanoparticles remains a challenge. I developed high performance liquid chromatography (HPLC) methods to probe the surface chemistry of Cornell Prime dots (C’ dots), a class of ultrasmall (<10 nm) fluorescent silica nanoparticles composed of an inorganic core with a covalently encapsulated fluorescent dye and coated in a covalently attached poly(ethylene glycol) (PEG) layer. Using a combination of characterization techniques such as gel permeation chromatography (GPC), photobleaching, and fluorescence correlation spectroscopy, I showed that the HPLC method that I developed is sensitive to single dye substitutions in the PEG layer of the C’ dot. I then used 2-dimensional GPC coupled HPLC to determine the size dependent surface chemical heterogeneity of C’ dots. Using this information combined with molecular dynamics simulations I proposed a mechanism for the condensation of dye on the surface of the C’ dot cores during synthesis and ameliorate this heterogeneity by changing the charge of the dye used in the synthesis. In addition to this I also studied the synthetic conditions under which optimal surface chemical homogeneity was achieved. This importantly shows that simply switching to a positively charged dye is not enough to optimize C’ dot surface chemistry and that dye dependent adjustments must be made. I have also developed additional methods to distinguish between the inner and outer surface of ultrasmall fluorescent silica nanorings (C rings) using HPLC. These methods can determine the location of a surface functionalization of the C rings and successfully differentiates between a dye conjugated to the inner surface and outer surface of the ring. Additionally, these HPLC methods can quantify the loading capacity of the inner surface of C rings, which may be critical for applications such as drug delivery. The extension from spherical inorganic-organic core shell nanoparticles to a different shape of inorganic-organic core shell structure highlights both the robustness of HPLC as a technique to analyze the surface chemistry of nanoparticles of a variety of shapes and the critical importance of surface chemical characterization especially when a nanoparticle has multiple surface types.