There is another thread in this forum titled Self-ISP on an Uno which covers this subject.
Please remove the thread.
Finally i fixed the problem. I used Atmel Studio for flashing.Finally my Arduino Self-ISP itself.Please remove the thread.
Why? Your solution may help others.
HoodLoader2 is not meant to be installed with Flip. It is a bootloader, not a firmware like HoodLoader. Read the HoodLoader2 wiki, especially the "Installation Sketch" page. That will give you a good understanding of how to use it. Also, the "Self-ISP on a Uno" will work on a R3, but yes you do need either a ISP, another Arduino, or a Usb-Serial convertor.