A cloning manager preserves in-place file system objects during a clone operation. The cloning manager determines boundaries of a file system to be created by the clone operation, and identifies at least one protected area within the boundaries, reserved for the file system. The cloning manager also identifies at least one in-place file system object within or overlapping the boundaries to be preserved during the clone operation. The cloning manager ensures that each object to be preserved is not located in a protected area, shifting the objects as necessary. The cloning manager creates the file system during the clone operation only in locations that do not contain objects to be preserved.