Nanoporous materials have attracted tremendous interest, investment and effort in research and development due to their potential applications in various areas such as membranes, catalysis, sensors, delivery, and micro devices. Controlling a nanoporous material’s microstructure is of great interest due to the strong influence on efficiency and performance. For particles, microstructure refers to particle size, shape, surface morphology, and composition. When discussing thin films, microstructure includes film thickness, crystal orientation and grain boundaries. In this respect, we focus to develop novel methods for the synthesis and characterization of nanoporous materials and their films, which are capable of controlling the microstructure of material. This dissertation is composed of two main sections and each explores the fabrication of a different nanoporous material: 1) A simple fabrication method for producing oriented MFI zeolite membranes with controlled thickness, orientation, and grain boundary; 2) A microfluidic synthesis of ordered mesoporous silica particles with controllable size, shape, surface morphology, and composition. The first section of this dissertation demonstrates a simple and commercially viable method termed the micro-tiles-and-mortar method to make continuous b-oriented MFI membranes with controlled membrane microstructure. This simple method allows for control of the thickness of the membrane by using plate-like seed crystals with different thicknesses along the b-axis (0.5 μm to 2.0 μm), as well as to manipulate the density and structure of grain boundaries. Microstructural effects of silicalite-1 membranes on the gas separation are investigated by measuring the permeation and separation for xylene isomers. In the second section of this dissertation, a new synthesis method for the ordered mesoporous silica particles with controllable microstructure is demonstrated. This novel method combines a microfluidic emulsification technique and nonaqueous inorganic synthesis with a diffusion-induced self-assembly (DISA). The systematic control of the particle microstructure such as size, shape, and surface morphology is shown by adjusting microfluidic conditions.