There's not too much you can do to get rid of the body aches from the flu other than wait it out.
The body aches should only last 2 to 3 days with the flu but you can try taking some over the counter pain medicine to help with the muscle and body aches.
A heating pad or heat packs to the pain areas which can help relieve the body aches.
Stay hydrated with the flu, get plenty of rest and use a humidifier or take a steamy hot shower.
The steamy hot shower can help add moisture to your lungs and help relieve muscle and body aches from the flu.