You can start with the DSPDBR command. You must specify the name and library for a physical file on your system. Remember, this is where the data is stored. This command will show you all of the "Dependent Files" that exist, regardless of the library they reside in. These files are the logical files or indexes that provide alternate sequences or views of the physical data.
Now that the indexes are identified, use the DSPFD command on each of them to display their "Access Path Description". Don't forget about the physical file. It may have a keyed access path or index as well. Each "Key field" and "Sequence" needs to be recorded for all of the access paths. Once this information is collected, you may find exact duplicates or some "near duplicates". Application software changes may be necessary before any of these can just be deleted.