By interfering two small diameter Gaussian laser beams, scanning beam interference lithography (SBIL) is capable of patterning linear gratings and grids in resist while controlling their spatial phase distortions to the nanometer level. Our tool has a patterning area that is up to 300 mm in diameter. The motive for developing SBIL is to provide the semiconductor industry with a set of absolute metrology standards, but the technology is easily adaptable to other important applications such as the making of high precision optical encoders. In this article, we describe a system for carrying out automated beam alignment for SBIL. Our design goals require tight alignment tolerances, where beam position and angle alignment errors must be controlled to ∼10 μm and ∼10 μrad, respectively. We describe our system setup, and discuss the so-called iterative beam alignment principle, focusing specifically on deriving a mathematical formalism that can guide the development of similar systems in the future. Repeatability experiments demonstrate that our system fulfills the alignment requirements for nanometer-level SBIL writing.