Siebel Administration >  Maintaining the Siebel File System - SFSCLEANUP utility

This is what the Bookshelf says about the Siebel File System -
The Siebel File System is a shared file system directory or set of directories. The Siebel File System stores document files, Siebel Configurator models, Web template definitions, and other files not appropriate for database storage. System user preferences are also stored in the userpref subdirectory of the Siebel File System.

The following list provides suggested best practices when dealing with the Siebel File System:
All Siebel Servers must have direct access to the Siebel File System. The only exception to this rule is when a server is running a Siebel Document Server only. If the File System Manager (FSM) is disabled on the Document Server, it accesses the Siebel File System through the FSM on another Siebel Server. In all other cases, the Siebel Server must be able to directly access the Siebel File System.
The Siebel File System can be configured to use multiple directories that may exist on separate devices or partitions. Before you configure the Siebel Enterprise, at least one file system directory must exist that you can designate for use by the Siebel File System.
There are few strict rules for deploying the Siebel File System. Theoretically, the file system can be hosted on any of the servers in the Siebel Enterprise or on servers in an independent file server farm. For small-to-medium deployments, a common scenario may be to place the Siebel File System on the Siebel Gateway Name Server. Implementations with a large number of attachments may need a dedicated file system server. Consider using a high-speed RAID disk storage system to increase file system throughput.
When using a large number of files in the Siebel File System (300,000 or more) in a Windows NTFS folder, disable short filename generation. For more information, see the Microsoft technical document about how NTFS works.
During normal operation of Siebel Business Applications software, it is likely orphaned files will be stored in the Siebel File System and that orphaned records will exist in the Siebel Database. Periodically run the SFSCLEANUP utility to remove orphaned files from the Siebel File System. This utility is located in the bin subdirectory within the Siebel Server root directory.

This is an example of how this command can be run

cd /app_folder/siebel/8.1/siebsrvr/bin
. ../siebenv.sh
export SIEBEL_REPOSITORY="Siebel Repository"

./sfscleanup /U sadmin /P password /C DSN_NAME /D siebel /F /app_folder/siebel/8.1/fs /X /tmp/sfscleanup-111102.log /R Y

the results will be like

Processing file system /app_folder/siebel/8.1/fs...
Opening cached file iterator...
Found attachments for S_ACCNT_ATT
Found attachments for S_ACTIVITY_ATT
Found attachments for S_AUDIT_TRAIL
Found attachments for S_COLLAB_CMD
Found attachments for S_DCP_PKG_ITEM
Found attachments for S_DOC_CORR
Found attachments for S_DOC_PPSL
Found attachments for S_LIT
Found attachments for S
Found attachments for S_OPTY_ATT
Found attachments for S_SRCH_MBLI_ATT
Found attachments for S_UPG_KIT
Found attachments for S_UPG_KIT_IARG
Found attachments for S_USERLIST_ATT
Found attachments for S_MKT_IMPRT_TSK
Found attachments for S_MKTIMPTSK_LOG
Found attachments for S_DOC_AGREE_ATT
Found attachments for S_EAI_QUEUE_ITM
100 % done. Processing INVALIDS_ORPHANS...
848/848 files processed. 0 error(s) encountered.
CURRENT: 189
ORPHAN: 580
ANCIENT: 54
INVALID: 25

Thats it. Run it regularly- depending on how many users use siebel and how many attachments/files you have.