A method of processing a target object is provided. The target object has an etching target layer, an organic film on the etching target layer and a mask on the organic film. The organic film includes a first layer and a second layer, the mask is provided on the first layer, the first layer is provided on the second layer, and the second layer is provided on the etching target layer. The method includes generating plasma of a first gas within a processing vessel of a plasma processing apparatus in which the target object is accommodated; etching the first layer with the plasma of the first gas and the mask until the second layer is exposed; and conformally forming a protection film on a side surface of the first layer; and generating plasma of a second gas and removing the mask with the plasma of the second gas.