Many ubiquitous pollutants in aqueous systems (chlorinated hydrocarbons, phenols, etc.) can be removed quite efficiently by entrapment in surfactant micelles through the well-studied membrane enhanced ultrafiltration process (MEUF). It is the common assumption that spherical micelles swell upon uptake of the pollutants. We show that uptake of specific pollutants (particularly phenols) results in a dramatic shape change of micelles from spherical to wormlike and vesicular structures. We have developed a facile follow up method where the entrapped species in surfactant microstructures becomes encapsulated in mesoporous silicas. The pollutant is therefore highly concentrated with a volume reduction of several orders in magnitude, and converted to solid materials for easy disposal. But additionally, the process results in the generation of functional mesoporous materials. The fundamentals of such entrapment, encapsulation are studied through a combination of small angle neutron scattering, cryo-transmission electron microscopy and X-ray diffraction. There are remarkable modulations in micelle characteristics upon entrapment, with transitions from spherical micelles to wormlike micelles and thence to spherical vesicles and enventually to wormlike vesicles. These structures which are then used as templates for ceramic synthesis, create modifications in ceramic mesoporosity which are correlated to the characteristics of self-assembly.