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We describe a method to correct the errors induced by viscous drag on the cantilever in macromolecular manipulation experiments using the atomic force microscope. The cantilever experiences a viscous drag force in these experiments because of its motion relative to the surrounding liquid. This viscous force superimposes onto the force generated by the macromolecule under study, causing ambiguity in the experimental data. To remove this artifact, we analyzed the motions of the cantilever and the liquid in macromolecular manipulation experiments, and developed a novel model to treat the viscous drag on the cantilever as the superposition of the viscous force on a static cantilever in a moving liquid and that on a bending cantilever in a static liquid. The viscous force was measured under both conditions and the results were used to correct the viscous drag induced errors from the experimental data. The method will be useful for many other cantilever based techniques, especially when high viscosity and high cantilever speed are involved.