We introduce IceFS, a novel file system that separates physical structures of the file system. A new abstraction, the cube, is provided to enable the grouping of files and directories inside a physically isolated container. We show three major benefits of cubes within IceFS: localized reaction to faults, fast recovery, and concurrent filesystem updates. We demonstrate these benefits within a VMware-based virtualized environment and within the Hadoop distributed file system. Results show that our prototype can significantly improve availability and performance, sometimes by an order of magnitude.