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Hi Manuel;
The answer to your question depends on a few variables:
1) Is your database system comprised of multiple files?
2) Is your system hosted on FileMaker Server?
3) What kind of structure clean up do you require?

My recommendation for cloning is to usually use FileMaker Server to handle it for you. From FileMaker server's admin console, you can set up a new backup schedule. When going through the steps to do that, it will ask you if you also want to save a clone. If you select this option, then your backups will have clones of all your files for you. FileMaker Pro also has the capability to create clones however. This is a good option, especially if you don't have server, and furthermore if your solution is a single file system. To take advantage of this feature, go into File>Save a Copy As, and use the drop down to Save a:" > Clone"