I was able to resolve the issue.
I downloaded the windows System Cleaner tool from here.
After running that with Admin privlages, I looked through the list till I found the UE4_Prereqsetup_X64 installed in the list. I removed it. After that I reran the UE4_PrereqSetup_x64.exe and it ran with out any problems. So just incase any one in the furture runs into the issue, download a system clean tool to remove old installed version of the MSI.