A 3D rigid assembly modeling technique is developed for stream of variation analysis (SOVA) in multi-station processes. An assembly process is modeled as a spatial indexed state transition dynamic system. The model takes into account product and process factors such as: part-to-fixture, part-to-part, and inter-station interactions, which represent the influences coming from both tooling errors and part errors. The incorporation of the virtual fixture concept (Huang, Proc. of 2006 ASME MSEC) and inter-station interaction leads to the generic, unified SOVA model formulation. An automatic model generation technique is also developed for surmounting difficulties in modeling based on first principles. It enhances the applicability in modeling complex assemblies. The developed SOVA methodology outperforms the current simulation based techniques in computation efficiency, not only in forward analysis of complex assembly systems (tolerance analysis, sensitivity analysis), but it is also more powerful in backward analysis (tolerance synthesis and dimensional fault diagnosis). The model is validated using industrial case studies and series of simulations conducted using standardized industrial software (3DCS Analyst).