I have been having similar problems with my ultimaker 2. I just got it a few days ago, and whenever I try to move filament, the extruder either starts clicking or eating away at the filament when it gets to the hotend. I am using the filament that came with the printer, and have used the atomic method several times to the point where I could see through the nozzle. I took out the nozzle and tried burning anything that was inside as gr5 said. I loosened the 4 screws attached to the print head and have even updated the firmware.
I have been able to print one or two things the size of the ultimaker robot, but whenever I try to start a bigger print with support I experience the clicking sound on the first layer. When it clicks, plastic stops coming out of the nozzle.
I am not sure what to do, and any help would be greatly appreciated.