A file cloning process allows for quickly cloning files within a filesystem, such as when a user makes a copy of a directory containing files and subdirectories of files. A priority based main queue is filled by a depth first traversal of the directory to be copied with work items corresponding to files and subdirectories. Worker threads refer to the main queue for file cloning, subdirectory copying and directory traversal. Files that have not been modified since a most recent checkpoint are cloned without issuing a checkpoint request. Files that have been modified since the most recent checkpoint are moved to a delay queue. Once a checkpoint of the file system completes, the files in the delay queue are then moved to the main queue to retry cloning thereof. A secondary queue is also provided to prevent worker threads from becoming deadlocked in the main queue.