Your best bet is to set the environment variables from within Perl first, then execute your other programs.

$ENV{PATH}     = "/bin:/usr/bin:/some/weird/bin";
$ENV{SOME_VAR} = "some value";

$output = `some_command that I want output for`;
system("some_command with output to STDOUT");
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Of course, if it's because of your PATH variable that you're having problems, you're far more secure doing something like this:

system("/absolute/path/to/some_command", "argument1", "2", $etc);
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