Maskless lithography systems (MLS) presented feature the digital mirror device (DMD) as the pattern generator to replace photomasks. Here 1.5-μm, 10-μm, and 20-μm line/space MLSs are developed. In the MLS, an 848×600 microlens and spatial filter array (MLSFA) was used to focus the light and filter the noise. The MLSFA produces light pads smaller than the 17-μm×17-μm micro mirrors of the SVGA DMD, and filters the noise produced from the DMD, optical lens system, and microlens array. This MLSFA is one of the key components for the Maskless Lithography System, and determines the resolution and quality of maskless lithography. A novel design and fabrication process of a single-package MLSFA for the Maskless Lithography System is introduced. To avoid problems produced by misalignment between a two-piece spatial filter and microlens array, MEMS processes are used to integrate the microlens array with the spatial filter array. In this paper, a self-alignment method used to fabricate exactly matched MLSFA is presented.