In a shell script, you can substitute any result into any aspect of the script by enclosing the routine in backquotes. For example:

$ export IE=`myScript.pl $someShellValue $etc`
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I'm not much of a csh user, but I believe it would be something like this:

% setenv IE `myScript.pl $someShellValue $etc`
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I really don't understand your last statement:

But since i'm outputing to screen a menu, that text will get into setenv.

. Would you restate it with different words, please.