As long as any process is "in" (to use a simple term) any part of a mounted file system, that file system cannot be unmounted (eg. safely removed).
By "in", this means... has a file open, has a directory open, or has any part of its working directory in the file system.
So, if you've opened your USB drive w/dopus, you'll need to quit dopus so that windows can eject the media. If you opened dopus from some other directory, then navigate your way into the USB drive, you'd have to change the working directory outside the file system to be ejected.
Unfortunately, this concept is a bit difficult to explain without understanding processes and working directories, hence the simplistic explanation above.