Surface modification of glass beads with a self-assembled monolayer of (3-Aminopropyl)-triethoxysilane (APTES) was investigated. Characterisation of the self-assembled monolayer was confirmed by a reaction between amine terminal groups and thionylchloride of Rhodamine-B dye using fluorescence microscopy. Quantitative 3-dimensional profiling was obtained for all modification processes by converting microscopic images to numerical values. The reaction steps were also analysed using infrared spectroscopy (FTIR).