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A method for the functionalization of surfaces within soft glass microstructured optical fibers has been developed, using self assembled monolayers (SAMs) of silane coupling agents. We demonstrate the use of measurements of the fiber capillary fill rate, as a positive test for a functionalized internal surface. A simple theoretical model is used for comparison with measured fill rates. During this work, adsorption kinetics for SAMs of octadecyltrichlororsilane onto lead silicate glass has been investigated. This work is a critically important first step for a plethora of applications in biophotonics, chemical fiber sensing as well offering promise for protecting fiber glass from degradation.