You can simply wash them in the regular machine cycle by placing them in the mesh laundry bag. Sometimes, some stains remain due to the type of makeup used. However, those stain marks would be purely aesthetic; the pads get cleaned and can be reused without any problem.  If it still bothers you, you can soak your makeup remover pads in an equal mixture of baking soda and peroxide for a few minutes before washing them in the machine in the regular cycle. You can also rinse your makeup remover pads with water after each use to remove excess makeup.