An encrypted USB flash drive is the safest way to carry sensitive files. Unfortunately, you cannot password protect your entire USB flash drive, like you can password protect your PC or phone. Secure tools all work with encryption. Unless you want to invest in an encrypted flash drive with hardware encryption, you can use freeware applications to achieve a similar level of USB protection. This article summarizes the easiest ways to password protect or encrypt files and folders on a USB flash drive. 1.