Fortifying provides an added layer of protection for your Silos, Defense Towers and Town hall, making them less suceptible to monster and catapult attacks. This in turn slows down your enemies and can greatly reduce resources and towers lost in a typical battle.
Fortifying expends a lot of time and resources, therefore it is recommended to focus on the most important buildings first.
The TOWN HALL
Fortifying your Town Hall is crucial as your objective is to protect it at all costs. Fortifying it will allow it to withstand attacks while your towers hammer the opposing monsters.
Next would be your Aerial Defense Towers(ADT) as they are crucial in protecting your Town Hall, and also the most effective against flying monsters ie Fomor, Zafs and Balthazar.
Note that Defensive Towers are inactive during fortification, so it is recommended NOT to fortify (or upgrade) your Defensive Towers all at the same time, and avoid fortifying/upgrading all of the Towers on one side of your yard as well as it makes your yard penetrable.
One tip is to move towers outside your yard for Fortification, putting another tower in its place. This keeps your defensive perimeter intact and can throw off the enemy monsters as they head to the fortifying tower first, while getting hammered from your perimeter towers.
A perfect example of this is replacing your fortifying ADT with a Sniper or Tesla tower so that your Town Hall remains protected on the inner defense grid while the fortifying ADT serves as a decoy on the outer perimeter. Once fortified, move it back into its rightful place!!
One of the best tips to consider is the Storage Silos. While fortifying allows them to withstand a greater amount of damage, it also works against your yard in one crucial way; consider that you are smart and have places your Bunkers and Quake Towers within range of your Silos, hoping to thwart an attackers catapult on-slaught. This only works if the Silos CANNOT withstand the catapult hit! So think about that for a second... fortifying your Silos so they can withstand a catapult attack only leads the enemy attacker to CATAPULT THEM so they can wipeout the nearby Defensive Towers...
If an enemy is foolish enough to catapult a non-fortified Silo, they will lose valuable resources and send you into Damage Protection very quickly, without you having lost all of your resources.