This paper presents a mask-aware multi-stage depth enhancement framework for digital documentation of historical timber surfaces using RGB–Stereo-IR fusion. Accurate geometric recording of aged wood features such as wooden knots remains challenging due to uneven illumination and weak texture. The proposed pipeline, which aims to stabilise depth geometry under uneven illumination and low-texture surface conditions, integrates object detection, instance segmentation and confidence-guided depth refinement across three stages: (A) TV(total variation)-regularized mask-aware refinement, (B) confidence-weighted multi-view fusion, and (C) patch-based stereo reconstruction. Experiments on historical timber beams under varying illumination demonstrate improved depth completeness and geometric consistency, achieving a residual standard deviation below 0.6 mm in bright scenes and stable reconstruction in low-light conditions. The framework offers a practical solution for depth reconstruction of cultural heritage timber, supporting more reliable feature detection and analysis.