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There are many Youtube videos showing different types of DIY rust repair.
Depending on the size and depth of the rust on the roof you might be able to sand it down to clean metal, add some body filler, and prime/paint/clear coat by hand and end up with a decent result in terms of appearance and future rust prevention.
With your fender, the rust you see actually started on the inside so the entire panel is almost certainly compromised. If that is the case the only repair is to cut away the rusted metal and rebuild the fender with new/clean metal. For some folks that's a DIY project but if you're asking here it's not for you. You can pay a body shop to do the job, but with a 2007 FIt the repair would be very expensive relative to the value of your car.
Just for a comparison point, I have an appointment in a couple weeks to have a small bit of fender rust (much less than what you have) repaired on my wife's Nissan Leaf, and the estimate to cut out the rusted metal, fabricate a new fender lip, and repaint and blend with the surrounding panels is about $1400. That's difficult to swallow, but the car is otherwise in mint condition and I know that if not repaired the rust will rapidly get worse.
Having said that, if all you care about is making it look a bit better from 20 feet away, you can use a wire brush to remove the flaky rust, use a rust converter to slow the spread, slap on some body filler to smooth it out, and hit it with some Rust-Oleum. You just have to accept that you haven't fixed anything and in two months or six months it's going to look even worse than it does now. Note that the DIY Youtube videos don't show you what their simple repair looks like a year later.
If you just want to slow the rust, you can do what my dad used to do with our farm trucks and regularly smear the entire area inside and out with axle grease. It will also keep people from leaning against your car. If that's too messy for you, you can do what my old landlord used to do and find the closest match colored Duct tape and cover it up. Very cheap and totally ineffective.