If you are using a J-Link EDU mini there are several ways to check. One that i have found is using the Atmel Studio 7. Upon opening the program navigate to Tools > Device Programing or Ctrl + Shift + P. Then select the tool to J-Link ( assuming you have installed the drivers already for jlink), Device to ATSAM3X8E, Interface to JTAG. You may then click the "read" button on the device signature. to test your chip.
Although unreleated to the question but, what happened why windows could not get device discriptor is because i mistakenly seat the chip by 90 degrees. Turns out its not the big circle that is the indicator for pin 1 but there is a smaller circle on a different side.
Guys, there is NO NEED FOR A BOOTLOADER if you are using the native port, i can even upload using the arduino IDE. Though you have to erase the code with a push button to upload a new one.