Since I encrypted my external hard drive it does not stop running after I press eject. It disappears from the sidebar in Finder but it does not stop running. I have removed it and connected it again several times and the same thing happens every time. Can this be harmful for the drive or is it ok to remove it even though it is still running? Is there anyway to fix this so that it stops running when ejected? Or is there another safe way to remove it if eject does not work? I have a MacBook Pro with OS X 10.9.5.
As long as your volume is unmounted, whether or your drive is spinning doesn't matter. The drive will usually spin down on its own depending on when it's set to "go to sleep."
When you eject, you have successfully unmounted the drive.
If you wish to confirm, in terminal, just issue the command
mount. If you don't see the volume name of the drive you had mounted previously, you can consider it unmounted.