Starting with Cuckoo Sandbox 1.2, which will be released soon, the old data cleanup tool will be deprecated in favor of a new cleanup method.
The old clean tool, still available, it is the clean.sh script in the tools directory. It is a bash script used to delete the data inside the storage directory (malware samples and reports), logs directory and db directory. The downside is that if you are not using SQLite database but MySQL or PostgreSQL and if you enable the MongoDB reporting module to store analysis results in MongoDB, clean.sh won’t clean up that data, leaving you in a dirty situation.
In Cuckoo 1.2 clean.sh has been deprecated and a new clean up method is provided, using the —clean argument when calling cuckoo.py:
$ python cuckoo.py --clean
Running this command all the data will be deleted: storage directory (malware samples and reports), logs directory, data inside any database configured and MongoDB data if the related reporting module is enabled.