Zeolite nanoparticles were organized into functional entities on SiO2 substrates and microfabrication technique was tested to form patterns of zeolite nanoparticles on SiO2 using the electron beam lithography (EBL). The effect of different techniques for efficient zeolite assembly on the SiO2 substrates was investigated. For this purpose, three different assembly techniques were tested. The first two methods are spin-coating (SC) and ultrasound aided strong agitation (US) methods, which were tested using bare and silanized zeolite nanoparticles. The third technique is the manual assembly method, which was also investigated using bare zeolites. All methods were facile in terms of experimental approach. Full coverage of the substrate was obtained after all three methods, however strong agitation (US) leads to better organization of zeolite nanoparticles. Among all techniques, manual assembly method lead to the most organized zeolite nanoparticles with full coverage. Although strong agitation (US) also results in organized zeolite entities, it was not found to be a suitable technique for EBL studies. Using the manual assembly method, it was possible to form monolayers of zeolite nanoparticles on SiO2 and to make patterns of zeolite nanoparticles by EBL, which offers a simple technique to engineer the surfaces for immobilization of biomolecules.