Clearing Hidden Files on an iPhone
Your iPhone can quickly accumulate data and files in the background, much like a computer does, by picking up data from Wi-Fi networks, websites and apps. While you can clear these files via your iPhone's Settings app, you have to use third-party software to remove hidden files from your iPhone's root directory.
1 Safari History, Cookies and Data
When you browse websites with Safari, your iPhone accumulates history logs, cookies and other login data. To clear these caches for privacy or security reasons, tap "Settings | Safari | Clear History | Clear Cookies and Data."
2 Clearing Network Settings and iCloud Data
Your iPhone saves Wi-Fi network names and passwords so that your device can automatically join them in the future. To clear network settings, tap "Settings | General | Reset | Reset Network Settings." Some of your iPhone's app information is stored in the iCloud. Open "Settings," tap "Usage," and then select "Manage Storage" to remove individual app data from iCloud.
3 System Files
Remove files in the root directory of your iPhone using third-party software such as iExplorer, PhoneView or DiskAid (links in Resources). These software solutions let you enable disk mode on an iPhone connected to your computer through USB. However, beware of deleting files you don't recognize, as they might be necessary for your iPhone's operation.