You can fortify Towers, Silos and your Town Hall after reaching Town Hall level 5. Fortifying increases the damage protection percentage of a building with each successive fortification level.
As of March 18, 2014, Fortifications are now unlocked after reaching lvl 9 Town Hall with tripled fortify time. Players who fortified before this update retains their Fortifications along their level. It is returned to level 5 with changed cost and time in March 22.