Long haired guinea pigs must be groomed. If they develop hairballs, guinea pigs cannot vomit them up. They can slow down the gut and surgery may be necessary (Theus et al., 2008). A diet with plenty of fibre will help prevent hairballs. There is also a paste that can be prescribed by your vet to speed up gut transit of a hairball.
Be gentle with the comb and/or brush. Don’t tug. Take your time to groom out any problem hair or consider cutting it out. In some long haired guinea pigs the hair growth on the rear end is long so the undercoat does have to be trimmed back there to prevent soiling. If it isn’t then it will quickly become soiled and knotted. Ask a guinea pig breeder to show you how to groom. Here is a useful video. Most guinea pigs enjoy being brushed but are less keen on grooming at the back end.
Guinea pig enthusiast Peter Gurney recommended standing the sows, the females, on a towel and holding them steady with the left hand on their backs. Un-neutered males should be trimmed on a towel on your lap with your left hand cupping their testicles. This is to make sure you don’t cut them by mistake!
Theus, M., Bitterli, F., & Foldenauer, U., (2oo8), ‘Successful treatment of a gastric trichobezoar in a Peruvian guinea pig,’ Journal of Exotic Pet Medicine, 17, 148-151. Abstract.