Precise boundary annotations of image regions can be crucial for downstream applications which rely on region-class semantics. Some document collections contain densely laid out, highly irregular and overlapping multi-class region instances with large range in aspect ratio. Fully automatic boundary estimation approaches tend to be data intensive, cannot handle variable-sized images and produce sub-optimal results for aforementioned images. To address these issues, we propose BoundaryNet, a novel resizing-free approach for high-precision semi-automatic layout annotation. The variable-sized user selected region of interest is first processed by an attention-guided skip network. The network optimization is guided via Fast Marching distance maps to obtain a good quality initial boundary estimate and an associated feature representation. These outputs are processed by a Residual Graph Convolution Network optimized using Hausdorff loss to obtain the final region boundary. Results on a challenging image manuscript dataset demonstrate that BoundaryNet outperforms strong baselines and produces high-quality semantic region boundaries. Qualitatively, our approach generalizes across multiple document image datasets containing different script systems and layouts, all without additional fine-tuning. We integrate BoundaryNet into a document annotation system and show that it provides high annotation throughput compared to manual and fully automatic alternatives.