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.

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