By mistake I make some changes to important system files to bring transparency effects in Mint . I don't remember exactly what i did but due to this all the icons in application area of Gnome Shell were appearing twice. I have solved my problem by following these steps.

1. Open terminal and type

gksudo nautilus

A new window will appear with administrative rights.

2. Open /var/lib/menu-xdg/applications/menu-xdg from that window. Files will have name something like this "X-Debian-Games-Toys-oclock.desktop" (This file will be shown as oclock application in Gnome shell). Delete the files having extension .desktop  whose icons are displayed twice (In my case I deleted all files).

3. Open /usr/share/applications

4. Delete duplicate icons or unnecessary icons from here.

Hopefully this will solve your problem.

Note: Instead of deleting files, move them to a new folder placed at different location as deleting files may cause problems or shortcuts may be needed in future.