How do I prevent someone from shutting my town down?

I don't think is is possible. Best to just drain your bank account of it's money before you stop playing for the day.

That's what I do, I just upgrade my board as much as possible, just leaving as little as I can in the bank to get raided.

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I disagree. The best way to stop them from shutting you down is to not give them anything to shut down. Wait until you have enough money to buy an entire level, then buy it and leave it blank after that until you can do it again. When they target you to shut you down, they see nothing but a blank field and cannot shut or attempt to shut you down.