I wouldn't do it with a regular expression, but this works at least on your examples:

use 5.010;
while (<DATA>) {
    chomp;
    /(?=.*username=(?<username>[^&]*))(?=.*id=(?<id>[^&]*))/ or next;
    say "username = $+{username}; id = $+{id}";
}

__DATA__
http://beta.websitename.com/tool/view/mb/file?username=anirudh007&id=4
+3242342
http://beta.websitename.com/tool/view/mb/file?id=3323213&username=anir
+udh007


username = anirudh007; id = 43242342
username = anirudh007; id = 3323213
[download]