Copy your files you want (such as backups/nandroids, photos and music) on the internal storage to your computer, boot into recovery and wipe internal SD card.
In cwm: its under mounts and storage
In twrp: select wipe, then advanced wipe and wiping the internal SD card should be an option
Once you reboot copy all of your files back to the device...then reboot the device once again and everything should be back to normal...minus the unwanted file/files
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