I have a ULINK2 debugger now i want to use it as a debugger in atmel studio dose it possible ? How?
if not how can i use it to program .HEX file to SAM3S ?
No, the ULINK's are just for Keil products, you can download HEX files by putting them in a donor project output directory. And perhaps with a debugger script and a LOAD command.
For ATMEL you'd want to look at Segger JTAG/SWD pods, or the SAM-ICE branded versions thereof