Methods used to stop a stalker are similar to those that can be used to stop any attacker. To protect yourself at home, try setting up security cameras as well as installing a burglar alarm. You should not need to live in fear so establish safety measures in your home that give you a greater sense of security. Other self defense methods you can use to deal with a stalker include being aware of your surroundings at all times and avoid following a regular routine.
If you are being stalked, start by talking to local law enforcement about your options and, if possible, talk to a lawyer about getting a restraining order. To increase your safety, you may want to look into self defense training.