A monodisperse, spherical mesoporous silica (Acid-Prepared Mesoporous Spheres, APMS) was prepared and then functionalized with two types of Fmoc (9-fluorenylmethyloxycarbonyl) terminated silanes with variable chain lengths. N-2 physisorption experiments indicated that, under some conditions, the pores of the solid were completely filled by the Fmoc-protected organosilanes. These blocked pores were then "reopened" by the cleavage of Fmoc groups with a piperidine solution. In contrast to the solution reaction, this deprotection reaction was much slower within the pores. The rate of deprotection was followed by UV/visible spectroscopy, and a plot of Fmoc released versus time showed a sigmoidal shape. An empirical model was applied to the data, which indicated that the reaction was influenced by the concentration and temperature of the piperidine solution as well as the number of Fmoc moieties within the pores. Using this information, we show that the location of the deprotection reaction in the pores of the silica can be empirically controlled. Our work provides a method by which the surface of the porous silica can be functionalized in a well-defined manner. This method can be used to produce materials for catalysis or drug delivery.