Abstract: Many high-resolution surfaces are created through isosurface extraction from volumetric representations, obtained by 3D photography, CT, or MRI. Noise inherent in the acquisition process can lead to geometrical and topological errors. Reducing geometrical errors during reconstruction is well studied. However, isosurfaces often contain many topological errors in the form of tiny handles. These nearly invisible artifacts hinder subsequent operations like mesh simplification, remeshing, and parametrization. In this article we present a practical method for removing handles in an isosurface. Our algorithm makes an axis-aligned sweep through the volume to locate handles, compute their sizes, and selectively remove them. The algorithm is designed to facilitate out-of-core execution. It finds the handles by incrementally constructing and analyzing a Reeb graph. The size of a handle is measured by a short nonseparating cycle. Handles are removed robustly by modifying the volume rather than attempting "mesh surgery." Finally, the volumetric modifications are spatially localized to preserve geometrical detail. We demonstrate topology simplification on several complex models, and show its benefits for subsequent surface processing.