The pilot reported that he repositioned the helicopter to load application chemical for the aerial application flight. The chemical was in a tank in a hay wagon and the tops of the hay wagon curved outward. He "slowly" set the helicopter down and felt the left skid touch followed by the right skid. The pilot lowered collective after the helicopter touched down and the main rotor blade struck the hay wagon. The helicopter "jumped" and shook violently. Both left and right windshields ejected from the helicopter and the main rotors came to a stop. The pilot attempted to shut down the engine; however, the engine continued to run. He exited the helicopter and applied the fuel cutoff. The helicopter sustained substantial damage to the main and tail rotors, the skids, and the helicopter "frames." The pilot reported that there was no mechanical malfunctions or failures with the helicopter that would have precluded normal operation. His safety recommendation stated that when setting the helicopter down near obstacles, recheck rotor clearance before fully lowering collective and be mindful that "the blades will move out of cone."