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Double-sided manuscripts are often degraded by bleed-through interference. Such degradation must be corrected to facilitate human perception and machine recognition. Most approaches to bleed-through removal rely on perfect alignment between the recto and verso images of a document. This paper presents a two-stage hierarchical alignment technique that can efficiently and accurately align the two sides of a document. Our approach first coarsely aligns the two images using a pair of anchors extracted from the recto and verso images respectively. The coarsely aligned images are then precisely aligned using block matching and radial basis function (RBF) based interpolation techniques. To evaluate the proposed alignment technique, we build a classification and recovery system to remove bleed-through interference and restore historical manuscripts. The accuracy of our alignment approach is then assessed with the accuracy of bleed-through correction.