Safely remove mechanism was changed since Udisks were upgraded from 1.0 to 2.0.
Previously safe remove switched LED on flash off and removed device from the system.
For now after Ejecting the LED on flash remains on. But it depends on flash model.
We have reported bug 1067876 about having Eject instead of Safely remove.
Previous versions of Ubuntu had nice looking application called Ejecter:
Description: application to unmount easily and safely external devices
Ejecter is a simple menu that sits in the system notification area, providing
you a quick way to unmount an external peripheral such as USB pendrive,
CD/DVD disk, external hard disk and so.
Ejecter will sleep behind the scenes and show an icon in the system tray when
one or more devices are connected to your computer.
It places its icon in notification area and allow to detach USB-device as in MS Windows. See screenshots (from here):
But is was removed from repositories since 14.04 LTS.
With some workaround we can get it working again on Ubuntu 16.04 LTS MATE and even on 18.04 LTS MATE (see this Q&A on AskUbuntu). But it does not spin-down USB HDDs.
On my systems I do the following: If I see only Eject option in the Caja window, then I launch GNOME Disks (
gnome-disks or from Applications→Accessories→Disks), select appropriate device and click Power off the disk button:
After doing so I see that LED on flash is off or USB-HDD is spinned down.
But it is very likely that it is paranoid solution since unmounting with ejecting is enough to keep data safe