Take out the food and water from the guinea pig hutch also. Using a dustpan and brush scoop the rest of the hutch contents into a bag for disposal later. If there are stubborn patches on the guineas hutch use a wallpaper scraper to clean these off.
When your have removed all the soiled bedding from the hutch, clean the guniea pig cage with a disinfectant suitable for the use with animals. They are usually readily available from pet stores and supermarkets. Make sure you use newspaper on the guinea pig hutch floor, it makes cleaning out so much easier. Just roll it up and all the soiled bedding will be inside. Then brush out the guinea pig hutch and spray as needed.
When you are spraying out the guinea pigs cage make sure you thoroughly wet the corners and the joints between the sides, to kill off any unwanted pests. Also, sweep out any cobwebs from the hutch in the winter as these create damp but they are great to leave in the summer as they keep the flys at bay!
If possible, wait for the disinfectant to dry and then replace the hutch bedding with fresh material and plenty of hay to burrow in. One happy guinea pig in a clean hutch.