In order to obtain virus-free plants through tissue culture the best method is -

When a plant is infected with a virus, the virus spreads through almost the whole plant body.
However, the apical and axillary meristems remain free of the virus, because the cells there divide very rapidly and have no differentiated vascular tissue through which the virus could move.
So the meristem can be removed and grown in vitro on a nutrient medium to regenerate whole plants that are free of the virus. This is meristem culture.
Scientists have succeeded in culturing the meristems of banana, sugarcane, potato and other plants in this way.
Anther culture is used to raise haploid plants, protoplast culture is used for somatic hybridisation, and embryo rescue is used to save hybrid embryos of distant crosses.
So the best method to obtain virus-free plants is meristem culture.