The lily is a symbol of St. Anthony and a reminder of his purity. The blessing of the lilies on the feast of St. Anthony stems from various stories of miracles with lilies.
The Prayer of Blessing is below and can be downloaded here (PDF):
Sign of the Cross
Let us pray…
God, the Creator and preserver of the human race,
the lover of holy purity, the giver of supernatural grace,
and the dispenser of everlasting salvation;
bless these lilies
which we, your humble servants, present to you today
as an act of thanksgiving and in honour of St. Anthony, your confessor,
and with a request for your blessing.
Pour out on them,
by the saving sign of the holy cross, your dew from on high.
You in your great kindness have given them to us,
and endowed them with a sweet fragrance to lighten the burden of the sick.
Therefore, let them be filled with such power that,
whether they are used by the sick, or kept in homes or other places,
or devoutly carried on one’s person,
they may serve to drive out evil spirits,
safeguard holy chastity,
and turn away illness–all this through the prayers of St. Anthony—
and finally impart to your servants grace and peace; through Christ our Lord.
Then the lilies are sprinkled with holy water.