The invention describes a method and apparatus for the modulation of an immune response for the removal of a foreign body in skin or a visceral organ. A fractional phototherapy device is used to produce an acute stimulus for the immune response. The immune response may be enhanced by applying an exogenous substance. The immune modulation may be targeted or directed toward the treatment of a particular foreign body through the creation and amplification of particular biological signatures. This invention is particularly appropriate for treatment of skin cancer, autoimmune diseases, inflammatory diseases, and fungi.