We present a system for automatically extracting hieroglyph strokes from images of degraded ancient Maya codices. Our system adopts a region-based image segmentation framework. Multi-resolution super-pixels are first extracted to represent each image. A Support Vector Machine (SVM) classifier is used to label each super-pixel region with a probability to belong to foreground glyph strokes. Pixelwise probability maps from multiple super-pixel resolution scales are then aggregated to cope with various stroke widths and background noise. A fully connected Conditional Random Field model is then applied to improve the labeling consistency. Segmentation results show that our system preserves delicate local details of the historic Maya glyphs with various stroke widths and also reduces background noise. As an application, we conduct retrieval experiments using the extracted binary images. Experimental results show that our automatically extracted glyph strokes achieve comparable retrieval results to those obtained using glyphs manually segmented by epigraphers in our team.