I did change my packages in synaptic from manually installed to Automatically (they were not manually installed but automatically). Now they are marked for Autoremove.

I tested it with sudo apt-get autoremove and the result is shown below (a reduced version because its almost all packages). I remember last year I had same issue and solved it via Ubuntu forums but the forum is down and I cannot reach the post! Anyone has any idea how to fix this?

sudo apt-get autoremove 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages will be REMOVED: 
  unity-asset-pool unity-greeter unity-lens-applications unity-lens-files
  unity-lens-music unity-lens-photos unity-lens-video unity-scope-gdrive
  unity-scope-musicstores unity-scope-video-remote unity-services
  unity-tweak-tool unity-webapps-amazoncloudreader unity-webapps-common
  unity-webapps-facebookmessenger unity-webapps-gmail unity-webapps-googledocs
  unity-webapps-googleplus unity-webapps-launchpad unity-webapps-linkedi
  xserver-xorg-input-wacom xserver-xorg-video-all xserver-xorg-video-ati
  xserver-xorg-video-cirrus xserver-xorg-video-fbdev xserver-xorg-video-intel
  xserver-xorg-video-mach64 xserver-xorg-video-mga
  xserver-xorg-video-modesetting xserver-xorg-video-neomagic
  xserver-xorg-video-nouveau xserver-xorg-video-openchrome
  xserver-xorg-video-qxl xserver-xorg-video-r128 xserver-xorg-video-radeon
  xserver-xorg-video-s3 xserver-xorg-video-savage
  xserver-xorg-video-siliconmotion xserver-xorg-video-sis
  xserver-xorg-video-sisusb xserver-xorg-video-tdfx xserver-xorg-video-trident
  xserver-xorg-video-vesa xserver-xorg-video-vmware xul-ext-unity
  xul-ext-webaccounts xul-ext-websites-integration y-ppa-manager yad zenity
  zenity-common zip
0 upgraded, 0 newly installed, 1440 to remove and 0 not upgraded.
After this operation, 3,853 MB disk space will be freed.
Do you want to continue [Y/n]?