One of the comments on the previous post reminded me of another free useful (Windows) tool - USBDriveFresher.
If you often use your USB drive between Mac, Windows and Linux operating systems, you might have noticed small, but numerous hidden system files left behind (Mac OS is particularly notorious for this). This simple app will automatically remove all files like .Trashes, .Spotlight-V100, .ds_store, ._*, thumbs.db and any others you specify.
Download: affinity-tools.com