Scientific discovery builds on accurate observations interpreted through domain knowledge and reasoning. For scientific 3D data, this requires understanding structures and spatial relationships, from protein contacts to anatomical organization. Existing multimodal benchmarks largely evaluate text and 2D images, while scientific 3D evaluations vary in representations and protocols across disciplines, limiting cross-disciplinary comparison. To assess these foundational capabilities, we introduce ScienceVision, a cross-domain benchmark for scientific 3D understanding and reasoning through expert-level visual question answering (VQA). We construct 250 questions, with 50 each from Biology, Chemistry, Medical Imaging, Mechanical CAD, and Architecture, through a pipeline combining synthetic question generation with domain-expert review and annotation. Each task pairs a native 3D artifact with a scientific question, a specified response format, and a task-specific reference answer, requiring domain knowledge to be applied to geometric or topological evidence. We evaluate 12 models on the same questions in three settings: visual question answering with native 3D artifacts accessed through an agent harness's file and code-execution tools; the same workflow augmented with expert-inspired viewer inspection and measurement tools exposed through the Model Context Protocol (MCP); and visual question answering from prescribed rendered 2D images using an agent harness. All settings use the same task-specific deterministic final-answer scoring. The inspection environment supports view changes, target isolation, and slice inspection. In this main comparison, the best mean answer score is 0.53 out of 1. Mean scores in the native-artifact workflow without additional MCP tools exceed those in the rendered-image workflow for every model, by 17.2 percentage points on average.

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