We present the fabrication of thin membranes with dense arrays of nanometer and submicrometer pore arrays by the integration of standard micromachining with three pore patterning techniques: electron beam lithography (EBL), nanosphere lithography (NSL) and aluminum anodization. Using a serial top-down EBL technique we exploit a fine size, positioning and flexibility of this tool. NSL and aluminum anodization, as self-organized bottom-up processes, guaranties cost efficiency and throughput. In our work, we have fabricated silicon nitride (SiN) and alumina (Al2O3) membranes with a thickness down to 100 nm, side length ranging from 200 μm up to 2.4 mm and pore size ranging from 20 nm to 500 nm.