As materials deposition technologies for digital fabrication evolve, the inevitable push toward volume manufacturing will necessitate the application of alignment and inspection technologies to monitor and control the production process. Many of these processes will depend on ink jet deposition of materials onto substrates with previously or subsequently applied structures or images. The successful function of the end product will depend on the precise alignment of materials from layer to layer. This paper describes the development of a Substrate Alignment Tool (SAT) using machine vision methodologies for rapid in-line measurement and adjustment of the alignment between layers. In addition, the SAT can double as an Image Analysis Tool (IAT) for in situ monitoring of process quality. This paper will focus on the design and use of the SAT for ink jet applications. Of particular concern to this study will be the identification of error sources and their contribution to process accuracy and repeatability.