Mesoporous materials with engineered surface properties are of interest for molecular separations, catalysis, drug delivery, and chemical sensing. One of the longstanding chemical challenges in the engineering of nanomaterials is to control the placement of different chemistries in spatially distinct regions on a nanoscale object. This thesis focuses on discovering and understanding processes to prepare such spatially differentiated chemistries on porous silicon. For the porous silicon system, the ability to prepare pores of average diameter anywhere from 1 to 200 nm allows the harnessing of surface tension and capillary forces to promote or obstruct the infiltration of reagent for selective modification. The first process investigated involves placing different chemistries on the pore walls by means of microdroplet patterning. In this method, a chemical resist is drop-coated on a porous silicon sample to mask distinct regions across the plane of the chip for subsequent chemical modification. Two chemistries, silicon oxide and silicon-methyl, are demonstrated here. The differential partitioning of test molecules on the resulting hydrophilic/hydrophobic film is achieved by simultaneous optical reflectance measurement of both regions, where the reflectance spectrum contains a convolution of the Fabry-Pérot interference spectrum for both types of surface chemistries. A second approach to engineer porous Si nanostructures that is investigated uses a hydrophobic organic liquid as a chemical resist; it is infiltrated into the pores to mask the interior of the porous silicon film, while the exterior surface and the pore mouths of the film are subjected to an aqueous chemical reaction with HF and subsequent chemical modification by thermal hydrosilylation. When chemically modified with a hydrophobic dodecyl species, the resulting film has a hydrophilic interior and a hydrophobic outer surface. The ability of these core-shell porous nanostructures to admit and release small molecules is assessed and exploited. The last portion of the thesis focuses on an evaluation of chemically modified porous silicon particles as oral drug delivery material, with an emphasis on the ability of the interior of the porous silicon nanostructure to protect physiologically unstable drugs. Partially oxidized porous silicon particles show no toxicity to nematodes at particle concentration up to 1 mg/mL in culture media. In vitro experiments show the particles protect anthelmintic protein-based drug Cry5B from hydrolytic degradation in simulated gastric fluid, and the bioactivity against nematodes is maintained. However, much reduced bioactivity of the therapeutic particles is observed In vivo on hookworm-infected hamsters. The lack of effectiveness in treating the disease In vivo is attributed to the short residence time of the particles in the gut of the animals.